I find this happens a lot, but I must say that I have the following steps, so it doesn't usually matter as in the broad areas where this might happen, I am going over with the base color again.
Prime
Basecoat color
Wash
Basecoat color (sometimes a mix of the next layer and base) leaving the recessed wash areas untouched
Layer
Layer
Highlight
But I'm painting yellow, which requires a lot of layering.
Also, I have decent end results after years of practice, but I am not a great painter, so I do a lot of touch ups. So listen to these other guys

. I think I need to try the varnish coats to save some headache.