That might be either the result of a patch or too large graphics.
Let's start with the latter: Outside of a couple special graphics, most of them in SMW are 4 KiB large (half a graphics page). If you ended up with more than that then you might end up overwriting the level data (the graphics are compressed and the buffer only has enough space for up to 4 KiB*). Lunar Magic should warn you if the graphics are too big.
How to fix this: Very easy: Avoid graphics which are larger than 4 KiB! You have to make a copy of a 4 KiB graphics file, move the content into a new file and if you're using YYCHR.NET (the new version which I guess you're using), chose no when you save the file (I'm very sure that's the case since there are around 32 tiles which end up filled with water).
*Actually, it's a bit larger but SMW just expects 4 KiB for most graphics.
More unlikely, if that isn't the issue then you should port your hack to a new ROM and add the patches one by one. That way you know which patch breaks what.