Repair turrets with building upgrade is incompatible with basically any mod that requires some "magic" processing upon placing and/or removing items. Tested so far: Factorissimo, Quantum Resource Distribution, Bulk Teleporters. For all of them, if the corresponding item (factory/chest/teleporter) is placed (or removed) by repair turrets (instead of by hand or by drones), it becomes unusable.
Another possible bug (or, maybe, some weird interaction with Squeak Through) - sometimes, when placing a blueprint, for some reason some trees don't get marked for deconstruction, but still prevent item placement. When that happens, repair turrets continuously try to place the item, which wouldn't be so bad on it's own, but, if I'm not mistaken, the items that fail to be placed just vanish, so it acts as a resource sink.