"I opened the big window and let the cool wind in."
There might be a single wrong character that you're missing, but the software is failing to recognise which one and underlining the comma instead. I had the same problem, but when I went through it I realised that I'd put あけて instead of just あけ, and it worked when I corrected that. It's a very easy mistake to overlook.
入る [はいる] (what you used) means "to enter" and is an intransitive verb, e. g. "I enter a room" = 部屋に入る [へやにはいる] and is used with particle に.
Intransitive means something is doing something itself. Another example is "窓は開く" (The window opens [by itself].
入れる [いれる] means "to let something in". It is a transitive verb, so something/somebody is doing this to something/somebody else. It is used with particle を, like in the example sentence here: "[私は]涼しい風を入れる" (I let the cold wind in.)
To put this into context using the window example, it is:
"I open the window." (窓を開ける) [transitive]
"The window opens [itself]." (窓は開く) [intransitive].
Hope this helps!