My guts tell me WTP doesn't handle proper dependency (re)deployment from a classpath library (The maven one in this case).
m2e-wtp doesn't do anything with regard to deployment, that's pure WTP's magic.
There's probably a way to reproduce the problem using maven-less projects but that probably requires some more head scratching.
Was the error popup a symptom in your initial observations (missing jars)?
Anyway can you please open a bug for the jar locking issue during redeployment at https://issues.sonatype.org/browse/MECLIPSEWTP?
I'll follow up with the WTP team when I can investigate.