I have same issue - certain areas can't be waterfilled... well.. in editor it sais "Noxys Waterfill" on the area, but is land and can't place waterpump on it.
Currently not using alien biomes, but a ton of other stuff - might have to look into it as anoying - strange is I don't think I have anything new, so must be an update in either Factorio or some mod that does this for this mod has worked flawlessly for many great year (thanks for mod!)...
PS!
Used this mod with Alien Biomes previously and not had any issues... but been a while.. 1.0 I think...
PPS!
Me again... OK - think I know what the issue is... seems that when I clear forest with grenades it leaves behind an "entity" called "Small Scorchmark". This seems to block waterfilling in that spot and area around it!!! When I removed them in the editor waterfilling worked like a charm in editor and in-game...
Think this is part of Factorio update - base/graphics/entity/scorchmark/small-scorchmark.png