I had this issue in Mothership raid, and later in a Winter Lord instance. in the MSR, I had my protector bots and battle drones summoned, but the assault bot just straight up said no. I tried over and over, made sure afterburner and PFF were off - nothing. I had no trouble re-summoning bots when they were killed, and tried twice to dismiss all and re-summon, but still only got the tier one and tier two pets to show up.
Later in the Winter Lord instance, I was standing in ouroboros with my bots summoned, and when I appeared in the instance, they were gone, and I couldn't summon ANY of them (and man did I try).
I did run other solo missions and some team 50+ team content later, and that all went fine.
I'm perfectly willing to accept it's something I did, but yesterday was the only time that stuff has happened to me.