It's possible they inserted it with the pin in the wrong position which would mean the rotor would be significantly out from where it should be.
To ensure the distributor is aligned correctly you need to ensure the #1 cylinder is at TDC on the compression stroke. In my TJ the mount for the non A/C pulley gets in the way. I use the #2 with the plug removed and feel for compression build up as the engine is cranked around by hand using the crank pulley nut. Firing order being 1-5-3-6-2-4, I then have to turn the crank 2/3 of a revolution to bring it back to TDC at the end of the compression stroke. This is done to ensure the distributor isn't aligned with #1 when the #6 is at the top of the compression stroke.
Once the position of the crank is known, the distributor alignment can be checked. As mentioned, when I replaced mine the alignment pin was in the 2.5L position and I had to move it to the correct position. With the crank in the correct position the rotor arm and sensor should be removed and the alignment holes in the rotor plate and distributor housing should be inline if it has been installed in the correct position. See diagram below for alignment positions.
If it isn't aligned, removed the mounting bolt and hold down and pull the distributor.
With the alignment holes properly aligned, the distributor can be slid in place. The drive gear is helical cut, so when it meshes with the cam the distributor turns clockwise by about an hour. The distributor has to be started with the bolt down tab an hour back so that when it's inserted it will align with the hole in the block. I find it a bit tricky on the TJ to get the hold down bracket in place but once bolted down it should be good to go.
Edit: I'd ask them if they have the old sensor still anyway. Explain it's common knowledge in the Jeep world that aftermarket sensors can cause problems, and it's recommended to fit the original sensor to new distributors where possible.
