[dcatn]

I know that you can't use ethanol in GC-MS analysis because ethanol will almost always have water in it which will harm the column but I found a study which extracted volatile compounds from leaves by mixing it in ethanol, filtering the slush, and storing it. The next paragraph then talks about GC-MS analysis. What am I missing?

[voidSetup]

It's fine to inject small amounts of water onto a GC column, especially for non polar columns.  Larger amounts of water can degrade the stationary phase of mid to high polarity columns such as wax columns.  You have to make sure though that your inlet temperature is high enough to completely vaporize the water and that the oven temperatures are high enough that it does not recondense.