Does this happen during training or quick missions? If it only happens on your saved games then you probably have a corrupted saved game file. I had this problem last week and did a lot of research on the internet only to find out that the SH series gets very finicky on the game saves. What I finally had to do was go back to an earlier game save (incidentally one that was less than 1.6mb in size) and proceed from there. Make sure you are surfaced and no time compression when you save the game.
If the lag happens during training or quick missions then you will need to post the OS and computer stats so we can see where you are.
Hope this helps!
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