Yes, and I found what: in my test module, the PC is on a bridge, and a pack of rats is between the catapult and the PC. The catapult therefore cannot use its melee attack, but since it finds a valid target (i.e. there's a path to go to it), it continues the attack and then switches to the spell system.
In the test I prepared, I removed the rats. When I tried, I got the same thing as what you described. So I also surrounded the catapult by unwalkable terrain in the next version: alas, the catapult was just doing nothing.
Finally, I gave it a thrown weapon: now, even if the walkmesh prevents it from moving towards the target, it can still attack from a distance. For best results, go to the middle of the bridge and attack from there, the catapult will react by throwing rocks. If you go closer, it will use its melee attack (I changed the distance in the 2da for testing purposes, modify the values of 14.5 and 16.9 to 4.5 to 6.9 [or even lower] if you don't want this to happen).
Note: as the projectile also does damage, it's possible you suffer both from the spell and the rock (just change the properties of the rock if you lose too many hp!)
Note 2: near the catapult, there's a strange blob. Could you have a look at it and describe how it animates for you? For me, the center is closing then opening (looping), which is what I wanted, but when PJ tried it it appeared to expand from the edge (in other words, the center would stay at the same diameter). Thanks.
Oops! Almost forgot! The test module (along with the override files you will need) is here.