I've read how you're supposed to be able to get the urn stones of people you're sim is close to/family of from the mausoleum but ever since I got the game I've only ever seen the stones of people my sims are enemies with. It doesn't matter if its a new game as I've seen it on several of them, it doesn't matter if its a sim I created or apparently if the sim is created by the game as once a townie moved in with my sim family and 2 siblings she was close to died, 1 a tot, 1 a child and still only enemy stones showed up. I wasn't aware at first I even had this issue until I'd read how people you liked were also supposed to be there, so anybody got any idea whats going on or how to fix it?

I'm not sure if it's mods doing this, but you should get any sim's urnstone in the mausoleum, regardless of your relationship with them. And you should be able to take them as well, if they're in the mausoleum inventory and not on the cemetery lot. The enemy thing might be just pure coincidence.

Only mod I can think of even remotely related is Master Controller, could it be the cause?

Definitely not, unless it's not the right version for your patch level. If anything, MC should ensure you get tombstones for ALL sims who die (I am not sure if service sims who die generate tombstones in the vanilla game, but they definitely do if you use MC).

Since you already have MC, you can kill off a random sim using Advanced / Force Kill, and see if their tombstone is in the mausoleum.

Yes, people force killed with MC have urns to go to the mausoleum yet still I can read about townie sim friends dying in the paper and nothing...

After thinking I did remember another mod remotely related to 'death' this one: http://modthesims.info/download.php?t=523924

Any possibility it could be the cause?