The fragment might sequester another factor required for vesicle trafficking or actin organization, rather than acting through Munc18. For example, binding a different SNARE-associated protein could lower the concentration available for productive endogenous complexes. This is a possible dominant-negative effect, not evidence that the isolated N terminus contains the entire SNARE interaction surface.
A less specific alternative is cellular stress or reduced viability. Those effects could suppress both invadopodium formation and matrix degradation without selectively inhibiting the proposed trafficking pathway.