Well, when you're using a gravel vac to siphon out water/clean substrate, you just have to be careful to keep the end of it down on the gravel bed and watch for any fish who are curious enough to get that close to the siphon.
Most fish will swim away from it but you do get the odd braveheart who gets a bit too close.
If by some chance a small fish happened to go up the vacuum and down the outlet tube, just put him straight back in the tank and examine for any fin damage. More than likely they will be fine, just a bit shocked, so keep the tank light off for a while to help calm them down.
Honestly, though, you don't want to be taking the fish out every time you do a water change. I mean, how often are you doing water changes at present? Weekly? Fortnightly? Monthly? It's a lot of hassle removing fish and stressful on them.
Unless you have a major ammonia/nitrite/nitrate problem in the tank, you shouldn't need to do more than small weekly or fortnightly water changes - 25-30% is about average. Some do slightly more, say 50%, but it all depends on the tank size, volume of water, the type of fish, how many fish, water quality etc.
Regards, Athena