1. As a writer, you may know what the shot or scene looks like in your head. Getting a layout or final page that is different than you imagined is very common. And it's not necessarily a bad thing. As long as the story is getting told effectively, let the artist do his or her thing.
2. Your script may not contain all the information you need on every panel description. If you can, read the script through twice before you start putting pencil to the page. Make notes on your script. If you see something on page 5 that affects page 3, note it on the script on page 3 so you're sure to include it. As the artist, the bulk of the responsibility of the story actually getting told falls on your shoulders.
3. Color and lettering notes in the script often get missed or ignored. Be patient with this, or if you can, email the whole team separately to make sure they get followed. As the writer (on creator-owned work in particular) your work and involvement does not end when you hand over a script. Be proactive, without being annoying to your creative team. Offer help.
4. If there is a disagreement between creators, if you've got an editor, this is a great time for him to step up and settle (or even better, prevent) arguments. A key role for the editor is to prevent the creators from getting agitated at one another. If you don't have an editor, remember this, don't email angry. Getting angry doesn't do anyone any good and blurs whatever the issue at hand is. Calm down, then write a tactful email.
Remember, this is a partnership of storytelling. Treating everyone on the creative team with respect, and considering all of their ideas, is always a good thing. As the writer or the artist, you probably have a clear vision, but that doesn't mean that others aren't talented or invested. In fact, the more they're considered and appreciated and their ideas are incorporated, the more "into the project" they become. And that's a great thing for everyone involved and the reader, too!
So there you go! If you're working with others, a lot of problems can and probably will come up. Keep these things in mind as you continue to work through them and you probably WILL work through them. Many a good project have met an end by creators arguing. And that stinks for everyone.
Happy holidays, everyone.