There is quiete a variety of possibilities I learned so far:

• वह दोपहर में घर आता है (using में)
• मैं शाम को जागती हूँ (using को)
• वह सुबह सात बजे जागता है (using neighther में nor को)

Can someone explain me which comes when?

Should this be सुबह मैं ?

Can the verb only be masculine here?

Why Duolingo put it as wrong when I said, "he wakes up in the morning at seven."??!!

Morning was not there in this question. This is unfear

"He wakes up at 7.00 in the morning" should be accepted!

7 am should be accepted