How old is that EOS3? It was reported that some of the early EOS3 had similar problems with metering as you described, Kay (about half stop underexposing). I belive some cameras manufactured from 1997(when production of EOS started) till April or May of 1999 can have that problems. I am sorry I can't remember specific details, my EOS3 was manufacuted after May 1999, and has no problems, so I didn't pay much attention on issue...
So, check metering as Rich described, and if meter was off, set permanently exposure compensation if needed(if you read manual it is easy to do). Smileguy has also valid point, same thing (thumb wheel on camera back accidently moved) happened to me few times. Thing is, if you accidently turn wheel on camera back same time when shutter button is half way pressed, camera will make exposure compensation. You can check that on exposure compensation flashing "broken" line on cameras LCD.
When I read what kind of photograph you made when you saw problem, I guess also next: have you compensate for water reflection of light? Reflective meters are easy to fool, and EOS3, despite having great meter, is no exception. So, could it be that water in thub reflected too much light, camera meter that reflected light, and you didn't compensate for that reflected light?
Good luck.