When cloning a selection with water contained by slabs and stairs, the water will pass through the slabs and stairs, treating them as if no blocks are there. To note, unsure if this is intended as you too are not able to place water on top of slabs (even when they are inline with a full block).
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Thank you for your report!
However, this issue is Working as Intended.
When a non-full block is cloned, its waterlogged state is part of the information copied to the new block. It's assumed that this is what you would expect in most cases, and there is currently no option to override it on the /clone command. (Even if there were, it wouldn't solve the problem in general, because you might want to copy the waterlogged state for some blocks but not others,)
Quick Links:
📓 Issue Guidelines – 💬 Community Support – 📧 Customer Support – 📖 Game Wiki
Thank you for your report!
However, this issue is Working as Intended.
When a non-full block is cloned, its waterlogged state is part of the information copied to the new block. It's assumed that this is what you would expect in most cases, and there is currently no option to override it on the /clone command. (Even if there were, it wouldn't solve the problem in general, because you might want to copy the waterlogged state for some blocks but not others,)
Quick Links:
📓 Issue Guidelines – 💬 Community Support – 📧 Customer Support – 📖 Game Wiki