If you have a bad bottle of gas, you will typically see traces of oxygen and nitrogen. Water tends to condense at high pressure, so you are not likely to see that in carrier gas until the pressure in the gas bottle is very low.
If your plumbing to the instrument is new or has become contaminated, you can see moisture - and that is good reason for an indicating trap close to the back of the instrument.
Unless you have reason to suspect the gas supply, let's give some thought to the GC!
Check all fittings for leaks. If there is an open path, diffusion will run up stream. Be sure the instrument is leak tight. And be sure you have a good septum on the inlet. (I have seen replacement of a corred septum resolve the moisture level in a mass spec.)
If you have very low GC head pressure, you can get water diffusion back through the split vent. (It to is a leak - in a way.) A high split ratio will increase the flow away from the GC. Set the GC inlet to split mode and set a split ratio of at least 50:1. See if the water level drops.