Hi Steven,
Wire removal can be tricky at times... It depends a lot on a few factors such as size in frame and what's behind them.
More information would make it a lot easier for me to help you with the problem. Perhaps you could upload a before and after movie clip up on Youtube? Or even post a few frames so I can get a better look at what you are fighting with?
Is the camera locked off (on a tripod or braced on something so that it doesn't move) or moving?
If it isn't locked off than you won't have what we call a "clean plate" which can be sourced to replace the image that is obscured by the wires. If not, no worries, we rarely get good clean plates on wire removal shots anyways...
If you do not have a clean plate to work with than typically we try to "fill in" the wire by either blending in nearby pixels and or sourcing image information from another point in time in which the wire is not covering those exact pixels.
If you don't do a very good job of this you end up with what you are seeing in which you will see colors jittering around in the area that you have made your paint out. If you've simply tried to paint back the information as you could with the paint or clone tool this is the problem that you can expect.
There are some good tools out there to help you with your task. It's been some time since I used After Effects to remove wires. (Now I use Nuke) I believe I used a plugin that was specifically designed to handle wire removal. You would simply set the tool to either end of the wire and it would use one or more of the previously mentioned techniques to clear out the wire from the frame.
I did a quick google search a found a few links for you to try out.
Link One - Making one "clean" frame in photoshop and tracking it back into your scene instead of trying to paint it out frame by frame or by using a plugin.
Additionally, you may find the first half of this
"analyzing motion" tutorial helpful where he explains how to track a still image into a moving background plate.
Finally, you might also want to check out Steve Wright's article,
Invisible Effects.
Good luck!
Mark