I'm currently working on a custom mine and encounted a problem setting up the mining of the ore, I've set up a Pickaxe Mining Marker and created a Linked Ref between the Ore Vein and the Marker, but while testing it in game the mining animation will play but cut out as soon as it start not letting me get any ore from it, I have several in the level all with the same problem.

Chance are I'm missing something basic out, usually the root of all the problems.

Try copying a working ore vein from one of the game cells and then pasting that into your cell. You can then change the ore type and orientation but the references remain. I've never had any success building a working ore vein from scratch for some reason.