After this cold spell I notice that some of the panels on my MX5 have small bubbles in the clear coat. I was wondering if anyone has had this problem and can it be solved without a re-spray.

Little tiny 1-2mm microblisters and lots of them?

It was either damp weather when solvent basecoat was applied, or waterbased basecoat that was not fully dried, either way there's not a lot that can be done as usually it lifts the lacquer and basecoat away from the primer.
If the blisters are very minor they may be less noticeable with warmer weather, but it will get worse in the long run.
Usually the old basecoat will require complete removal before respraying as otherwise it can show up in the repainted panel.

I have seen on older cars it being caused by use of a car cover in direct sunlight pushing moisture into the paint, i'm not sure if that is only a cellulose paint problem or if it affects 2k as well.

Dave