Electrical Confusion

mholmen

I am putting in a new bath fan into my bathroom. Currently there is a light over the sink, a light near the shower and a fan near the shower. There are two switches near the sink that control the two lights & 1 switch near the shower that controls the fan.

Where the confusion lies:

Turned the lights and fan on in the bathroom then went to turn off the circuit. When I turned off the circuit only the two lights went off (fan stayed on). Hunted and found that the fan was tied into a different circuit (same circuit as all overhead lights in the house). since I wasn't working with fan yet, I left that circuit on and went to work on the two light switches. I plan on replacing the the two switches with a double switch and outlet. Took out the two light switches and this i where I got a bit confused. In the box there were four wires coming in, and my assumption was 2 lights, 1 power, 1 to further down circuit. Also all grounds were tied together and all neutrals were tied together, only black was attached to switches. Well, I used a non-contact tester and I didn't get any beeps, however after I removed the blacks from the switch and started removing neutrals I got a small spark and everyone in the house started complaining about lights flickering. Turns out that I had two separate circuits coming into the box. The hot wire from each circuit were tied together and then had a hot wire coming out of them and into the switch, then all neutrals tied and all grounds tied. When I removed the neutral and ground from that second circuit part of that second circuit was dead? Why would someone wire it this way, and what can I do? I want to put a gfci in (i believe it is required) but it constantly trips if I tie in both circuits the way it was, and if I separate the circuits, the second circuit doesn't work? If I put a regular outlet in, it does work, but this whole circuit just makes me very nervous now.

Thanks
Matt