I'm creating acts from my recollection of Man of Steel:
Act 1: Krypton (prologue/not really a flashback/recounts Superman's extraterrestrial birth).
Act 2: Grown Clark Kent (present day) rescues oil rig workers with superhuman abilities.
Flashback 1: Clark is in elementary school, exhibiting superhuman abilities like super hearing and heat vision that surprises him.
Flashback 2: Clark is in junior high, exhibits superhuman ability of super strength/Jonathan tells him of his
extraterrestrial birth and challenges his son to explore the world in order to discover his purpose in it.
Act 3: Clark re-appears after rescuing the oil rig workers working in a diner. He overhears a possible clue about an extraterrestrial object being studied in the Artic and heads there. Side note: Pig pisses him off and Clark decides to trash his rig before hitting the road.
Act 4: Lois Lane arrives in the artic to report on the mysterious object. She meets Clark for the first time because he arrived there and got a job before she flew in.
Act 5: Lois witnessed Clark's superhuman abilities of x-ray vision and heat vision. She didn't care much for his heat vision though. Clark leaves Lois to be rescued and he flies off in the Kryptonian ship.
Act 7: Lois makes her way back to Metropolis but her account of what happens gets stonewalled, so she slips the story to a competitor.
Act 8: Meanwhile, Clark passes all the identity verification tests that the ship puts him through and he finally discovers his Kryptonian heritage, his purpose that Jor-El wanted for him, and fully tests his superhuman abilities like flight for the first time.
Act 9: Lois starts her search to discover Clark's identity by going back to the artic, gets clues about the diner, heads there, gets clues about his job as a fisherman (e.g. customary Pulitzer Prize winning investigative work), tracks Clark back to Smallville, and asks him to let her tell his story. He starts explaining his fear based upon Jonathan's concern...
Flashback 3: Clark witnesses his human father act heroically to save others and perishes in the attempt because Jonathan loved his son so much he prevented Clark from saving him. He sees Jonathan would rather die to protect his son's secret until it was safe for the rest of the world to accept him.
Act 10: Lois accepts Clark's reasoning, returns to Metropolis and Perry, who's pissed about her leaking out the story but glad she's letting it go due to the story's implications and public reaction.
Act 11: Clark tells Martha about his Kryptonian heritage.
******
That's it. With the exception of Zod's "telepathic" explanation to Clark explaining his group's arrival on Earth and later discernment of the Codex, there aren't any other chronological interruptions in the film from Act 11 forward.
Flashbacks are an established method of continuity editing. They can be bothersome sometimes. Personally, I think Snyder's flashbacks and montages (another form of continuity editing) in DOJ were more bothersome but MOS never lacks continuity.