Construction site 'stomping' is standard behaviour.
"You can remove enemy construction sites by moving a creep on it." - Construction Site Documentation
I noticed you have towers that won't firing on the enemy creep. Are they an ally, or were you just ignoring it since it didn't have any attack parts?
If they're an ally, you may wish to ask them to first check if there's an allies construction site where they plan to move, or add it as an impassable position if they use a custom cost matrix with their path finding.
If you were just ignoring it because it had no attack parts, note that some player purposely program their creeps (especially scouts made from a single MOVE part) to 'stomp' enemy construction sites, so you should still be wary of them.