Funimation hasn't tampered with anything there. That's the normal flow of the anime.
But to help you out, here's the story progression in sequential, normalized form:
Starting point (SP): Haruka confesses, Takayuki eventually takes things seriously (EP1)
... Things progress well. (EP2)
SP+1 month: Haruka has the accident. (EP2)
... Haruka in coma, Takayuki rattled (EP5)
SP+1 year: Takayuki loses it, Mitsuki makes her move. (EP5)
... Lukewarm relationship between Mitsuki and Takayuki (EP3)
... Mitsuki cuts her hair
SP+3 years: Mitsuki wants to move in together with Takayuki (EP3)
... Mitsuki and Takayuki run into Akane (EP3)
... Akane informs Takayuki that Haruka came to (EP4)
... They visit Haruka, Akane tilts on the two (EP4)
Got it?
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