The enemies warping in from behind you is normal on that mission, it's not really a glitch so much as something that simply happens.
If you watch your radar you have a bit of time after they spawn to kill them before they can attack you.
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Unfortunately you can't. They spawn in instantaneously and you are immediately dead. I had this similar problem and its a bit of a cheap move. Give at least some time for us to respond to a threat coming, much like how the Minotaurs on the Nexus just before entering it. At least you can manage that but on Sempik Prime is full of crap. Just out of nowhere and pretty much a death sentence.
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As soon as I realized they spawned up there during phase 2 I've always kept and eye out for them and haven't been killed since. The don't just auto spawn and attack, you do have a small window and all you have to do is stagger them.
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Understandable to an extent, but most of the enemies who spawned behind me don't even register on the minimap (ie Stealth vandals). I guess the only exception is that one Dreg? But then again I don't think I was alive enough to even react to it. You can't really blame me to much for assuming the wall I had my back up against was suddenly going to turn into bad guys. lol I was more focused on the actual path of approach to my perch and less so on the hilariously impossible, I guess. I'll be sure not to employ this tactic again. As the community says about pretty much anything, I'll "get gud" and "lern 2 play" like the scrub I am. :D
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Just turn into the dead end of the tunnel with the train (move completely to the end) or move back where you came from. Those are the most safe spots for this part of the mission. Of you chose the train spot, hide behind the train when the third wave appear or make yourself invisible.
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At least 2 Stealth Vandals will teleport onto the platform if they can't path to you. Games like WoW and SWG death with this and it's the most annoying thing ever. Bungie should remind them that Fallen are capable of jumping.