they're probably not completely "out of phase" - as in, phase-flipped. It's more likely that they're not time aligned.
The snare mic is far far closer to the sound source than the overheads, so the snare hit arrives at the close mic before it does on the overhead microphone(/s).
You can either tweak the location of the mics a bit until you find a good compromise, or use the appliance of science, by delaying the snare channel so that it perfectly lines up with the overheads (or, slip the overheads earlier so that they line up with the snare).
This technique is used almost always when recording classical performances in large venues, and I'm not entirely sure why it's not "the done thing" with drum kits. I tried it many years back, and found that it really adds a solid low-mid BANG! to the snare, so I stuck with it.
I find that it can help the toms cut through a bit as well, but in my drum room, there's insufficient low-end from the bassdrum being picked up to cause any issues, so the bassdrum doesn't cause much concern. Time-aligning it can add a more defined attack to the bassdrum sound, however.