make structure in picture 1 and save it on structure block.
remove stairs so water flows. picture 2
then reload structure block original.
notice how it water logs blocks that weren't water logged before. picture 3
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Thank you for your report!
We're tracking this issue in MC-140270, so this ticket is being resolved and linked as a duplicate.
That ticket has already been resolved as working as intended, which means this is not considered a bug and won't be fixed. Please do not leave a comment on the linked ticket.
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Please reopen as this is a different bug than other report. This bug is about flowing water (not water sources) becoming water logged sources when loading structure blocks. It creates massive hindrance when using structure blocks.
next to or inside
not just inside; the first stair block will be next to a water source block, so it gets waterlogged, then the next block is placed, it's next to a water source, so waterlogged.
Additionally, you didn't specify anything about you refering to flowing only, you literally just said "if there is water", which means it's the same thing and you're just now trying to make it distinct.
Duplicate of MC-140270, WAI.