Seeing as you just closed this issue without making any attempt to get more details about reproducing the error and there is no way for me to reopen this bug report, I have created a new report for the same issue.
Yes, the bug is that 'fill water replace air' should only replace AIR with water but it's replacing waterloggable blocks with their waterlogged variants, it should not touch anything that is not AIR. Screenshots and world attached for your reference.
Just replacing the block with a non waterlogged block of the same type is preposterous given how many variants of stairs plus direction/orientation there are.
Erm, I created a copy because the original report was marked resolved when it has not been resolved. There's no way to reopen the original issue so what do you suggest I do?