This has never happened before, but last run some of the enemies went invisible in certain areas and I fought them that way. Over all, I enjoyed the glitch and found that it made the game much more fun.
I filmed it as well, so have at it. Well, have at it in like 15 minutes. Its still uploading.
Oh, and if it's important, I'm running the game through Steam, but I'm not playing on a Steam account. Playing with Windows 7, most updated Java, all old editions of Java have been erased, etc. I do NOT have the "Cull Transients" option enabled.
---the Thorn Jab Jelly became invisible and 5-6(approximate) seconds later, I was killed.
I just encountered this issue as well. I was doing Rise or Fall, and towards the end of the first room of arena, the mecha knights appeared invisibly. I thought it was a glitch that the healer spawned by itself, but then I started losing health rapidly to enemies I couldn't see. Or rather, I could only see then as they were shielding. VERY difficult to gun fight, and impossible to sword fight. They continued appearing invisible for the rest of that round (including 2 mecha knights that I had spawned from capsules), and things got very glitchy in the last room. After I loaded into Haven, I closed the game window and restarted it. I tried the mission again, and everything was normal up to arena. Then the enemy knights were all invisible again... I was running with someone new to the mission, so I warned them about the layout for the 3rd floor. I was completely prepped to kill one of the two final healers when suddenly ALL enemies were invisible. As I was lying there dead, I could hear the sound effect of the healers mending, but I could see nothing else. That, and my party member appeared to be shielding when his health showed that he was dead. None of my friends were online to come save me that time, so when we both died (quickly), time ran out and we returned to haven.