Capo's are an imperfect mechanism, an most guitar necks have imperfections as well. There are a few techniques to keep in mind when compensating for this.

One; it's easy to guess wrong about which string/s isoff when you capo, so you may end up making your guitar off if you're not careful - that is; you'll be in tuned with youself, but off with the rest of the world, and much worse off when you remove the capo - so you must stay accurate (to A 440, that is). Before you capo, be sure you're precisely in tune.

Two: place the capo carefully - just below the fret, squarely and without letting the strings get pulled to one side or the other. Try it a few times, watch carefully, learn to reduce the stress in the worong direction.

Three; learn which fret placements, and which strings are most likely to be off. I suggest using an electronic tuner while experimenting during practice at home ... know your guitar and you'll know how to fix it quickly and accurately on stage.

Four: Try to resolve intonation problems without adjusting the tuning with a capo, first. Again, with careful placement of capo, being sure you're in tune to start without the capo - and then if your still, for example th bass string/s is a bit sharp (and this is the most common complaint) rather then adjusting the tuning peg/s, try bending/stretching the string with the capo in place. Push down hard on the string straight down to the sound hole - it sonds a bit drastic, but it will actually pull the string from under the capo and lower the pitch - and probably when you remove the capo, you'll still be in tune.

Five; if all else fails, retune with an electronic tuner iwth the capop in place. Remember this is the most dratsic thing you can do, and may have you retuning significantly every time you mo the capo. But if you gotta, you gotta!