Space Marine recruits spend years as scouts before becoming full Battle Brothers. How are all these Marines so green that they have never seen combat before?
The comic which comes with the special edition actually explains this. They've been very recently promoted from scouts but most of their actions were focused upon recon on the previous world they were on. Severus needed all his best troops to hold the line against a Tryanid invasion and needed a unit to perform a recon mission on the shrine world. Most of the comments about them comes from a lack of experience in full scale battle or true familiarity with some weapons they use.
Another possible explanation is that Captain Severus didn't consider them to be Ultramarines until after the rookies graduated from scouthood. Entirely possible that this is their first mission as full Space Marines.
It is. They were scouts in the prequel comic. And Severus says this is their first time in combat as Ultramarines, not their first time in combat.
Even so, it seems odd the Ultramarines stops just in front of an ideal ambush-position to argue. The squad has a horrible attitude to each other which seems evident in their showing during combat. Only the truly inept Black Legionaries actually makes the Ultramarines look like winners.
So, if they jump to Warp, the daemon will destroy Macragge. Why didn't Ultima squad just head to the bridge and tell them to stop?
It's a big ship. They might not have had the time to get there.
Also, he's the Captain of the battle barge. He's in overall command. Two newly ordained battle brothers won't be able to override his orders.
Space Marine captains don't run ships, that responsibility goes to the shipmaster (who gets that title to avoid confusion).
Are there seriously only a dozen Marines onboard the entire ship when it first arrives, that at no point Proteus can call for help? "Yeah, there's a daemon running around the room containing our holy artifacts, could someone maybe get down here?"
Well Space Marine ships don't have a very large a crew (compare to Imperuim ships) although it should have at least some squads of Ultimar PDF.
Why didn't the Imperial Fists fortify their little castle? Since, y'know...it's kind of their thing.
Unless Regal Dorn or another Space Marines chapter is actually present, the Imperial Fists tend to fall into the group of chapters that exist solely to get wiped out to show how tough the enemies are. Imperial Worfs?
They did fortify it and held against the Black Legion just fine. It was when a Warp Gate opened inside their defensive lines that things got "a little difficult".
Remember, we're not looking at the fortress in its prime. We're looking at a fortress that remains after three solid weeks of combat between Space marine/Guard forces and Chaos Space Marines. The fact that anything is left standing at all is a testament to the Imperial Fists' engineering and fortifications.
Oddly enough, a full burst from a boltgun at point blank range in the tabletop game has maybe a one in five chance of killing a power-armored Chaos Marine. So what's with all the one-shot kills and clean bullet holes in peoples' armor?
Similarly, an Apothecary in the tabletop game gives people a 1/2 chance of ignoring any hit they take. The Apothecary in the movie didn't seem to do a lot...
The reason Apothecaries give a 1/2 chance of ignoring any hit they take is because they are medical officers, the same thing happens with Imperial Guard medics in the tabletop games, and is supposed to account for their ability to heal wounds. Their main duty however is to collect the gene-seed of fallen battle brothers which he is seen doing multiple times, he is also seen helping to heal Severus and Hypax once they return to their strike cruiser.
Gameplay and Story Segregation. Bolters are one of the most notorious offenders of this - their tabletop rules make them merely average against anything tougher than a standard human soldier. In lore, they are basically a hybrid of an assault rifle and a small rocket launcher and do a lot more damage. Games Workshop famously once released rules for playing Space Marines on the tabletop as they're presented in lore; a single squad (and one tank) was expected to stand against a full army on the other side (and could actually do a pretty good job of doing so).