Which Version are you using?
Select the asset and "View Errors and Warnings" It will then either validate and remove the fault or it will tell you what is wrong with it.
Geoff
Errors in red should be repaired. The ones in yellow can be ignored or will disappear when the red ones are corrected. Some are easy to fix some are not. Someone posted a guide to repairing common errors in 2006 some time ago. The main benefit is better frame rates and few, if any, error messages or crashes while running trainz. Repairs are made using the editor function in CMP. Don't forget to commit or the changes/corrections will not take effect.
I think the standards of "error" vs "warning" in 2010 may be a little stricter then they need to be. Here's an amusing example of an error that I highly doubt would prevent the object from working:
Error: The Tag 'amazing' is not permitted within a container of type 'traincar'.
Whether it has any performance penalty or not, I'm not really qualified to judge.
As far as faulty dependencies, right click and choose "view dependencies." Then click "view in main list" and then you can inspect the faulty objects.