What version of m2e-wtp and JBT are you using?
m2e-wtp 0.12.0, which enables webresources support works with JBT 3.2.x
m2e-wtp 0.13.0, which is compatible with Indigo works with JBT 3.3.x
In any case, this is not a JBT issue but a m2e-wtp one, so if a bug report is needed, you should use https://issues.sonatype.org/browse/MECLIPSEWTP