On my test Quay registry I have emptied it of all repo's, and a month later the registry size on disk is still showing the images using space:

[ansible@quay registry]$ ls -al
total 8
drwxr-xr-x. 4 1001 root 35 May 9 00:57 .
drwxrwxr-x+ 3 ansible ansible 22 May 9 00:57 ..
drwxr-xr-x. 170 1001 root 4096 Aug 5 23:12 sha256
drwxr-xr-x. 2 1001 root 6 Aug 6 10:27 uploads

[ansible@quay registry]$ du -sh *
7.1G sha256
0 uploads

The logs show that garbage collection is running:

gcworker stdout | 2021-08-24 09:37:41,362 [65] [INFO] [apscheduler.executors.default] Running job "GarbageCollectionWorker._garbage_collection_repos (trigger: interval[0:00:30], next run at: 2021-08-24 09:38:11 UTC)" (scheduled at 2021-08-24 09:37:41.361041+00:00)
gcworker stdout | 2021-08-24 09:37:41,379 [65] [INFO] [apscheduler.executors.default] Job "GarbageCollectionWorker._garbage_collection_repos (trigger: interval[0:00:30], next run at: 2021-08-24 09:38:11 UTC)" executed successfully

and yet my registry is still consuming 7.1Gb even though it has nothing in it.

One of my customers has also noticed this issue.