There was a suggestion Ander Herrera was offside in the build-up to United's first goal, while there were some appeals for Rojo to be sent off for a challenge on Matteo Guendouzi, but Emery refused to blame the officials for costing his side a win.
Aaron Ramsey also came off with an ankle injury at Old Trafford, but Emery said "it's smaller than Rob's" and that the Wales worldwide will also be assessed on Friday.
Having been at Pep Guardiola's side during City's 100-point season there were plenty of calls from fans in north London to give the former midfielder his first head coach role.
Koscielny has taken part in regular training sessions with Arsenal's first-team and Emery is hoping to play the France worldwide against Qarabag next week.
"We could not control the game like we wanted for the 90 minutes, but for the second half it gives us confidence this draw". We were playing against a very competitive team and I think our spirit is good.
This isn't to say the Gunners played badly - some of their attacking play was excellent.
Lingard established himself as a key player for club and country last season as Jose Mourinho's men finished runners-up in the Premier League and FA Cup, before helping England reach the World Cup semi-finals.
"The second half, I think our players worked to win".
"I think we believe as a squad", he said.
'We're on the right way with him, he played two matches with the U23s and our plan is maybe can play against Qarabag, ' Emery said.
"He's working with us every day in training and playing in the under-23s with good feeling".
"Every supporter needs to feel that with us, and push like they pushed against Tottenham".