Is it possible you've inadverdently created the effect of a pair of three-way switches, but with the lights on two different paths instead of on the same path which is what you'd do if you were *trying* to make two lights controlled by a pair of three-way switches.
My idea only makes sense if it's not something more dangerous - like a ground fault.
Like KOK328 said, we need more details - is any breaker tripping, or can you walk back and forth repeatedly turning one light on (but causing the other to turn off). Any noises or smells would be an important (and bad) sign.
If so then you have what is called a switch loop. This is where you have a power in and out of a light, thats two wires, and a wire that goes to a switch. Generally a white wire in the light box is tied to the two black powers, and goes to switch, and comes back on the black wire to be hooked to light. The other two whites are neutrals and hook together with white from light fixt. If any of this makes sense you could pull down light and have a look. Then if its greek you could tell us what you see in there then we could surely help ya out. Good luck.....