Peter and Harley could have separate labs if they Peter asked for them, but they like working together. They have different strengths and it's a lot less intimidating to ask a kid your age for help when you get stuck.
On top of that, while Peter darts around and figures things out as he goes, Harley fully forms most ideas in his head before he gets to the lab, gathers what he needs, then stays in one spot until he's done. Usually. Harley's ideas don't always work, but he does usually have the right parts, he just needs to change how he uses it. Again, usually.
Today however, Harley got stuck, and Peter was in his own little world so he was no help, and he decided to tinker with some new stuff, but that involved getting up. What he wasn't expecting, was for Peter to also need something in the same spot, and not realize he was there until he was two inches away.
So Peter jumped, and attempted to steady himself using the nearest upright thing, which was Harley. But Harley isn't the most stable thing to use, so instead they both ended up on the ground, Harley half laying on Peter.
"You know, I'd weirdly always imagined you on top."
"Wha- I- sorry, I didn't realize-"
"Relax, no harm, no foul."
It was right as Harley pushed himself up to be straddling Peter that Tony Stark decided to walk in.
"Hi, Mr. Stark."
"Not in the lab."
"But it was-"
"Not in the lab."
"Get off him, kid."
"It was an accident, Tony."
"And yet you're still on top of him. On the floor of my lab. Get up, both of you. This isn't what I pay you for."
"Do we get paid?"
"I take snacks from downstairs, does that count?"
"I didn't even think we were employees."
"Okay, you're not Avengers, you're children. I'm going to leave, but just know I do have security cameras, and if I ever see you using the lab for things other than what it's meant for, those privileges will get taken away."
"So we're not employees."
"Just get up!"
With that, Tony left, and Harley finally rolled off of Peter and gave him a hand.
"So... you've imagined me on top?"
So, my understanding of Peter's spider sense is that it's kinda like Daredevil but with sight. Like, it's not a new sense, just the standard ones incredibly enhanced. But he can also let his guard down? So while he can tell where Mysterio is and avoid getting his brains blown out without seeing him in a battle, he can also get hit by a banana from May in his own home.
What I'm trying to say is Peter can still get scared because he didn't expect to see Harley because the lab is a safe space and he wasn't using his senses like that.