No they actually did not. I'm just gonna repost my analysis video from some pages back:
MGSV: A Phantom Plot (A Critique of MGSV's Story)
But just to make a short list:
-Why did the parasites seem to turn people into zombies?
-How did Skullface plan on getting so many mini-nukes?
-Why do the Skulls Unit members look all pale, sickly and insane but Quiet and Code Talker are perfect in every way?
-Why are these parasites never heard of again when they seem superior in every way to Nanomachines?
-Why did Ocelot need to hypnotize himself? His sole incredible attribute is the fact that he's a spy.
-Why does that cutscene in which you first meet Skullface make no sense? Watch it again. He somehow managed to teleport Saelthropopluosion into Smasei Fort without us or the Soviets seeing or hearing in about two seconds. Why did he bring it to Smasei Fort? To stop us from getting a rocket launcher? Then why didn't he kill us? Why did he have the Skulls Unit kill the Soviet at Smasei Fort when at that point the Soviets still believed he was working for them?
-Why can't Quiet just speak in Navajo, use sign language, Morse Code, tap, blink one for yes, two for no?
-How did the GZ medic get implanted with all of BB's memories? Ocelot was only present for a part of Snake Eater, wasn't with Snake for Portable Ops, and I doubt the medic from GZ was there for those totally private moments in PW.
-How does there exist technology to totally change a persons face and skin color to match another person?
-Why would anyone in XOF follow Skullface when he plans to destroy the English language and XOF is an American Spec Ops group?
-Why didn't Huey just tell us right away where Salethropdick was from the start?
-What happened to Eli and the kids? Don't link me the cut content, if it isn't in the game it's not explained.
I think you get the point.