Mobius' echo of "let time pass" reaching Loki and making him tear up confirming he was watching over Mobius.
Mobius leaving the TVA because Loki isn't there anymore.
Mobius being completely miserable whereas Sylvie is seen happy and care free and time hopping with only a "it's weird that Loki's not here, isn't it?"
Loki going to seek Mobius first for comfort when faced with the moral dilemma of choosing who lives and dies.
Loki staring at his hand wistfully, with tears in his eyes while he watches Mobius slip away.
Mobius being the first to notice something was wrong when Loki started walking towards the loom.
The fact that Mobius was present when Loki said "I know what kind of god i need to be... for you" means the director(s) and writer(s) are seeing him as a possible romance arc in the future for Loki that's why they put him there with Sylvie to claim plausible deniability.
The season one kiss being retconed.
Loki not killing Sylvie (which he contemplated at first) means he wants to give her the chance to go write her own story like she's always wanted without running. And we can see her being happy (without Loki) at the end because she's finally free.
At the end, Sylvie is comforting Mobius because he's hurting more and evidently more miserable.
It still irritates the hell out of me how well Sylvie seems to have accepted Loki's absence. I mean, come on, Loki SACRIFICED himself so that in the end she could come back and live her happy life the way she wanted. But in this scene she seems to be talking about the fucking wind, they ruined her so much in this second season.
While Mobius seems SAD AS HELL. ALONE in a new life that he still doesn't know how to deal with and that he didn't ask for, without the presence of the person he liked most. He looks so devastated, like someone came and destroyed his favorite jetski, when in fact the only thing destroyed was his and Loki's chance to ride that damn jetski TOGETHER.
Loki's inner transformation is strikingly prominent. He's not the absolute chaos that he was when he was brought to the TVA for the first time.
His kindness, gratitude and selfless love surface during his stay in the TVA. His unwavering faith in his newfound family in the TVA is all the proof we need. He never gets tired of defending and appreciating his loved ones.