You have never seen a situation where someone is concerned for a person's well-being, even if that person insists they're fine with doing something stupid, reckless, or seemingly out of their character to date? It's perfectly normal and common behavior.
But that said, the shower scene specifically has Lena provide her reason not to join in her internal monologue:
Python:
v "What are you standing there for? Why don't you join us?"
if ian_lena_couple and v10_ivy_sex:
"I had to stop myself from stepping into the shower."
"It was hard not taking up Ivy's offer, especially after what happened that night at her place..."
if v8_holly_sex == "lenaivy":
"This wouldn't be the first time the three of us got a bit naughty with each other, but things were different now."
elif v8_holly_sex == "ivy":
"This wasn't the first time I watched Holly and Ivy get naughty with each other, but I still couldn't join them."
else:
"But I knew I shouldn't. I couldn't."
"Getting naughty with Ivy in the privacy of her home was one thing, but getting it on with Holly too, in a public place..."
"How could I justify that to Ian? No, this would break our relationship for good."
jump v11showerleave
Now sure, you could argue that Lena who's been cheating shouldn't care about this. It makes some sense, too. But apparently this just isn't a route EK is interested in covering. Just like she's apparently not interested in providing path where it's Ian in relationship with Lena cheating on Lena by fucking Holly behind her back, even if he's cheating on her with other girls. (and i don't see you complain how this doesn't make sense, even if it's straight equivalent)
Or maybe you will get such scene down the road when it is in "privacy of home" and not in public shower, who knows?
Or, far more simply, it was a bug which was patched out, just like multiple other situations where scenes which weren't supposed to happen did happen as results of script errors. These things aren't always spotted/reported immediately, and it can get a while to have them fixed. It doesn't mean this was a dev suddenly changing their mind on the issue.