I have found the root cause of the issues it was just a bug with one of my mods that allows you to respec skills ("I'am the commander" was it's name I think) so to avoid the issue do not respec a already purchased/active reaction skill to not trigger this bug. You can respec reaction skills as long as you have not purchase it yet.

recreated a soldier and tried a combination of reaction skills (sentinel and rapid reaction) with covering fire and it works perfectly :)