Why would she be worried about her bringing a girl home? Saying roommate over girlfriend... I get the vibe they broke up but remained friends?
I'm...confused? This is our main couple right...? Sudden time skip and they're not acting like a couple...or what's happening?
Blastaar was right, if two girls don't carry a sign with "we're girlfriends" written on it at all times, there will be people who won't be convinced they're dating even after it's been explicitly spelled out.
Let's slowly go through it then. The first use of 'roommate' by Aya is there to narrate to the audience that her and Mitsuki's living situation has changed since we last saw them. Her assuming Mitsuki brought a girl home is a comedic reaction to Mitsuki being caught off-guard by Aya walking in while she's setting up the home theater because Mitsuki feels awkward about having bought it without Aya's permission. The second use of 'roommate' by Aya is said in this context because expenses like that should be managed by both. When Mitsuki acts cool to shake Aya's nagging off, there's a drawing of an arrow piercing Aya's heart, showing she loves Mitsuki no matter what. I hope this helps.