Bobby wasn't dumb enough to freeze first and ask questions later, but in a situation like this it paid to be on his guard.
Xavier calmed him and Logan with a telepathic message, while taking the diplomatic approach with Magneto and ... Long-Haired Guy.
Bobby's ice layer dissipated. He was going to show them he could be peaceable ... though he didn't need to be iced up in order to deep-freeze something. This was a show of lowering his weapon, but not dropping it completely.
Because seriously, tea and chess? Were they supposed to believe that's all Magneto wanted? Why bring Long-Haired Guy?
The Long-Haired Guy reacted to Logan in a way that suggested he was a telepath. That wasn't good news at all. In fact, it was entirely possible this was a fact-finding mission; with Magneto's knowledge of the mansion and Long-Haired-Guy's telepathy, he could potentially learn a lot.
When had he become Cyclops, anyway? That kind of paranoid logistical thinking was more Scott's bag.