There are a couple things that may be worth trying to resolve this:

• Uncheck the Steam Option : Steam > Settings > In-Game > Second Option "Use the Big Picture Overlay when using a steam input...
• Delete font files from C:\...\documents\Neocoregames\warhammer martyr\fonts\
• Try lowering 'physics detail' and 'character detail' as well as 'persistent bodies' and 'shadow detail' down to zero in the visual settings
• This Reddit thread may also help you if nothing else does: https://www.reddit.com/r/40kinquisitor/comments/g9e50x/fix_if_you_have_microlagstutter_on_a_nice_pc/?rdt=43879

Some additional possible fixes:

• Play in Borderless Mode, turn on v-sync and triple buffering in your GPU driver, turn it off in-game
• Drop the shadows to 0 and enable frame blending, you can set all the other settings to max and get a mostly constant 60 fps

Let me know if any of these did the trick or no!

Is this happening on all missions now? Or was this moreso a one-off thing? 

Either way, please, first of all verify the integrity of your game files on Steam, as demonstrated here.