Have any of you run into problems with water pushing enemies through fortifications? It has happened to me more then once.
Catchpockets can help. (In the following diagram, O represents a wall, X is a fortification, . is an empty floor tile. I assume water input is from the left, but I'm not sure it matters.)
OOOOOOOOOOOOOOO
OOOOOOO.OOOOOOO
...OOO.OOOOOOOO
OOOXOXOXOOOOOOO
OOOO.OOO.......
OOOOO.OOOOOOOOO
OOOOOOOOOOOOOOO
Critters flushed through a fortification will tend to end up trapped in the small two-square pockets between the inputs and outputs - they have to get pushed through multiple times to escape. Scale diagram up to match your desired level of paranoia about this bug's frequency.
To prevent issues on the inputs, I sandwich the serially-arranged flow-control floodgates between fortifications to keep building destroyers off them. I then use multiple floodgates on the same lever, arranged so the water must pass through
all floodgates to enter. Failure of a single (or even several) floodgates due to a beast getting pushed into the works doesn't stop the system from working correctly - it will be shut down by one of the other floodgates, as it is multiply redundant. Even a building destroyer can't wreck the system.
the downside is that it can take some time to set up a system of this nature, so it's better suited to a mature fort, or one where you have time to set up.