Hello!
The mod and game does not intentionally make the bots not able to cross the water. The bots use the same movement method as the biters, and same code for pathfinding, so i'm not sure why the biters can get over the water but the bot army can not.
Is there a way you can landfill the swamp to make a bridge across it? Or is it like an entire biome of shallow water? It's possible the alien biomes mod somehow modified biters specifically to allow them, but it doesn't know to also automatically modify the robot army units to add the same feature.
I would suggest you use the flying robot units in the meantime, but in the current release of Robot Army I think because they use the factorio 'unit group' feature they can't path-find over water or walls.
in my development build which is available on Github you could try backing up your save game, and trying to load that newer version (still in development!!!) and use the flying robots there, which act individually and DO pathfind over water and player's walls.