There was a Dev post about it. They asked if it was settings too low and when people responded it was occurring with high settings, he said that he added it to the "to do list". I'm paraphrasing, but the short story yes, they know. I lost the link, I'll dive through the Dev Tracker if you want.
I think its happening with borg shooting at me too, cause i never see any energy bolts flying at me, i just occasionally notice a borg raise his arm at me.
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I just noticed it in a mission a few moments ago.
All I could find, dstahl has seen it at least, but didn't state that it was indeed a bug.