Steps to reproduce:
1. Create new Seam Project
2. Seam Web Project page, Next
3. Java page, Next
4. Web Module page, Next
5. JSF Capabilities, click download library
6. Download JSF 1.2 Apache Myfaces
7. Finish project creation
8. Deploy project

There is error "Both MyFaces and the RI are on your classpath. Please make sure to use only one of the two JSF-implementations."
ASSUMPTION: Deployment should be working or specific configuration forbidden or at least some warning

12:50:47,001 ERROR [MyfacesConfig] Both MyFaces and the RI are on your classpath. Please make sure to use only one of the two JSF-implementations.
12:51:02,352 INFO [config] Unsanitized stacktrace from failed start...
com.sun.faces.config.ConfigurationException: Factory 'javax.faces.application.ApplicationFactory' was not configured properly.
at com.sun.faces.config.processor.FactoryConfigProcessor.verifyFactoriesExist(FactoryConfigProcessor.java:304)
at com.sun.faces.config.processor.FactoryConfigProcessor.process(FactoryConfigProcessor.java:219)
at com.sun.faces.config.ConfigManager.initialize(ConfigManager.java:335)
at com.sun.faces.config.ConfigureListener.contextInitialized(ConfigureListener.java:219)
at org.jboss.web.jsf.integration.config.JBossJSFConfigureListener.contextInitialized(JBossJSFConfigureListener.java:71)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3910)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4389)
at org.jboss.web.tomcat.service.deployers.TomcatDeployment.performDeployInternal(TomcatDeployment.java:333)
at org.jboss.web.tomcat.service.deployers.TomcatDeployment.performDeploy(TomcatDeployment.java:150)
at org.jboss.web.deployers.AbstractWarDeployment.start(AbstractWarDeployment.java:462)
at org.jboss.web.deployers.WebModule.startModule(WebModule.java:118)
at org.jboss.web.deployers.WebModule.start(WebModule.java:97)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:157)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:96)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:668)
at org.jboss.system.microcontainer.ServiceProxy.invoke(ServiceProxy.java:207)
at $Proxy38.start(Unknown Source)
at org.jboss.system.microcontainer.StartStopLifecycleAction.installAction(StartStopLifecycleAction.java:42)
at org.jboss.system.microcontainer.StartStopLifecycleAction.installAction(StartStopLifecycleAction.java:37)
at org.jboss.dependency.plugins.action.SimpleControllerContextAction.simpleInstallAction(SimpleControllerContextAction.java:62)
at org.jboss.dependency.plugins.action.AccessControllerContextAction.install(AccessControllerContextAction.java:71)
at org.jboss.dependency.plugins.AbstractControllerContextActions.install(AbstractControllerContextActions.java:51)
at org.jboss.dependency.plugins.AbstractControllerContext.install(AbstractControllerContext.java:348)
at org.jboss.system.microcontainer.ServiceControllerContext.install(ServiceControllerContext.java:298)
at org.jboss.dependency.plugins.AbstractController.install(AbstractController.java:1633)
at org.jboss.dependency.plugins.AbstractController.incrementState(AbstractController.java:935)
at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:1083)
at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:985)
at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:823)
at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:553)
at org.jboss.system.ServiceController.doChange(ServiceController.java:689)
at org.jboss.system.ServiceController.start(ServiceController.java:461)
at org.jboss.system.deployers.ServiceDeployer.start(ServiceDeployer.java:163)
at org.jboss.system.deployers.ServiceDeployer.deploy(ServiceDeployer.java:99)
at org.jboss.system.deployers.ServiceDeployer.deploy(ServiceDeployer.java:46)
at org.jboss.deployers.spi.deployer.helpers.AbstractSimpleRealDeployer.internalDeploy(AbstractSimpleRealDeployer.java:62)
at org.jboss.deployers.spi.deployer.helpers.AbstractRealDeployer.deploy(AbstractRealDeployer.java:50)
at org.jboss.deployers.plugins.deployers.DeployerWrapper.deploy(DeployerWrapper.java:179)
at org.jboss.deployers.plugins.deployers.DeployersImpl.doDeploy(DeployersImpl.java:1448)
at org.jboss.deployers.plugins.deployers.DeployersImpl.doInstallParentFirst(DeployersImpl.java:1166)
at org.jboss.deployers.plugins.deployers.DeployersImpl.doInstallParentFirst(DeployersImpl.java:1187)
at org.jboss.deployers.plugins.deployers.DeployersImpl.install(DeployersImpl.java:1107)
at org.jboss.dependency.plugins.AbstractControllerContext.install(AbstractControllerContext.java:348)
at org.jboss.dependency.plugins.AbstractController.install(AbstractController.java:1633)
at org.jboss.dependency.plugins.AbstractController.incrementState(AbstractController.java:935)
at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:1083)
at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:985)
at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:823)
at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:553)
at org.jboss.deployers.plugins.deployers.DeployersImpl.process(DeployersImpl.java:783)
at org.jboss.deployers.plugins.main.MainDeployerImpl.process(MainDeployerImpl.java:699)
at org.jboss.system.server.profileservice.repository.MainDeployerAdapter.process(MainDeployerAdapter.java:117)
at org.jboss.system.server.profileservice.hotdeploy.HDScanner.scan(HDScanner.java:371)
at org.jboss.system.server.profileservice.hotdeploy.HDScanner.run(HDScanner.java:256)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:317)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:150)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$101(ScheduledThreadPoolExecutor.java:98)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.runPeriodic(ScheduledThreadPoolExecutor.java:181)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:205)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619)
Caused by: javax.faces.FacesException: org.jboss.seam.jsf.SeamApplicationFactory
at javax.faces.FactoryFinder.getImplGivenPreviousImpl(FactoryFinder.java:606)
at javax.faces.FactoryFinder.getImplementationInstance(FactoryFinder.java:472)
at javax.faces.FactoryFinder.access$400(FactoryFinder.java:139)
at javax.faces.FactoryFinder$FactoryManager.getFactory(FactoryFinder.java:796)
at javax.faces.FactoryFinder.getFactory(FactoryFinder.java:306)
at com.sun.faces.config.processor.FactoryConfigProcessor.verifyFactoriesExist(FactoryConfigProcessor.java:302)
... 68 more
Caused by: java.lang.InstantiationException: org.jboss.seam.jsf.SeamApplicationFactory
at java.lang.Class.newInstance0(Class.java:340)
at java.lang.Class.newInstance(Class.java:308)
at javax.faces.FactoryFinder.getImplGivenPreviousImpl(FactoryFinder.java:604)
... 73 more