did you do a full compile? or did you stop it while it was doing portals (using task manager)?
water doesnt come in drops in source, it comes in brushes, thats your problem
Turn on everything in your map using visgroups, then open the texture browser, hit "only used textures" and then scroll though that list if you see any water texture you've applied one by mistake.
It's not the use of water textures. ctf_core uses no water and waterindicies is nearing 100%. I wonder if it's transparent textures that leads to this. It's stumped me since day one.
Waterindices are used when detail brushes touch structural brushes to smooth out their joining. They're related to T-junctions, as when you go over 100% you'll have too many T-junctions to fix up and it won't compile. Castle has about 99.6% waterindices, and I've gone over a lot