I wrote a test to reproduce an issue reported on SO and turns out this is easily reproducible. There seems to be a bug preventing deletes to be propagated to MVs in case a clustering key is used. See here for test case (testClusteringKeyTombstone should fail).
It seems MaterializedView.updateAffectsView() will not consider the delete relevant for the view as partition.deletionInfo().isLive() will be true during the test. In other test cases isLive will return false, which seems to be the actual problem here. I'm not even sure the root cause is MV specific, but wasn't able to dig much deeper as I'm not familiar with the slightly confusing semantics around DeletionInfo.