Several individuals , myself included have lost substantial amounts of material including rare items and major sub assemblies when the crafting mission either failed or was accidentally aborted.

If the mission fails I suggest that the materials be automatically returned to the players inventory.

Also Players should be warned if they are taking an action that might abort the mission like joining a group.

Yes

My vote would be to have it only return items for any deliver objectives that exist within the same stage where the abort happens. That way in a mission where you deliver 10 widgets, get a reward, then deliver 10 more widgets for a second reward, you can't just abort the mission after getting the first reward to get the first 10 widgets back.

If you mean "fails" as in a technical server side issue, sure... seems fair. However if you mean "fail" in the more traditional sense of you fucked up, then no... thats rediculous.

As for... "Players should be warned if they are taking an action that might abort the mission like joining a group."... yes, it would save new players or people who just don't know what they are doing some hassle.

The game does have a distinction between a mission "Failed", "Aborted" and "Interrupted"