According to the quest "Proper Tool Care", you can repair GT tools in an anvil, which doesn't work with the GT mortar.
Other tools like the saw can be repaired flawlessly.
In my case, I tried to repair a (Wrought) Iron Mortar, but I think this doesn't work with other materials either.
Im playing on the following commit from the 1.3-PR branch: 2ae6b4f

It's a bug, but it's a GTCE one. Moreover, since Omnifactory uses an outdated version of GTCE, we can't just report it to them without at least checking if it is present on the last version. Either way, Omnifactory likely won't be getting a fix for that until 1.3 (the GTCE update) at least.

From position of GTCE contributor I can inform you that Mortar as well as Plunger are not reparable.

Given that these items are not repairable in vanilla GTCE, going to have to say that this one's out of our control.