Oooooh yeah. Been there. Done that. Don't you hate it when you find things out "the hard way"? Ha-ha-ha! My guess is that you used two similar paints. In other words, your silver base coat was an enamel. Then when you brush painted the next color over it, that was an enamel as well. So basically the enamel in your medium green "reactivated" the enamel in your aluminum base coat causing the two to mix together and your paint brush just basically acted like a big mixing stick.
There is no problem whatsoever to use an enamel over an enamel. I'm currently working on Revell's 1/48 P-51B/C. I used MM Buffing Aluminum as a base coat and then applied the Neutral Grey and Olive Drab on top of that. I used an airbrush to apply my paint, though, because in doing so, you're just laying one color over on top of another. You're not aggitating the underlying paint in any way. In the future you might want to use the MM aluminum (enamel) as a base coat and then use acrylics for your color coats. The water-based acrylics will not react with the oil-based enamel.
On a side note, I think you'll find that half the people use primers while the other have don't. It's a personal choice. For me, sometimes I prime and sometimes I don't. Quite honestly, I think it's just dictacted by whatever mood I'm in at the time. IF you are going to prime, I highly recommend using Tamiya's primer in the rattle can. I tried it once on a whim and I was blown away at how smoothly it went on. It is absolutely phenomenal stuff.
While there's nothing wrong with using the MM aluminum as a base coat, you do have to keep some things in mind: MM aluminum is very glossy while something like the Tamiya primer, while smooth, still has more "bite" to it for the overlying paint to grab onto. As I found out, I accidentally applied the olive drab color a bit on the heavy side on my first few passes with my airbrush. The O.D. paint actually sort of pulled away from the recesses and panel lines due to surface tension. What I should have done was apply a light mist coat first in order to give the paint a rougher surface. That way, when I applied the next layer of O.D., the second layer would have a better surface on which to grab a hold.
I hope all this rambling helps and welcome to the forum!
Eric