Skythin

No. You only get the mastery points once for the initial leveling. Subsequent leveling does not gain mastery points again. Exceptions from this are kuva/tenet weapons (and the paracesis) and necramechs since these gain additional two level for each forma spent on them up to level 40 as the maximum.

It doesn't even though it should, its an UI bug. I picked up an arcane from a gruzzler during Deep Archimedia and it says "Deep Archimedia Reward", same as a real Archimedia rewards such as an Archon Shard.

Have one for sale, price is 300 plat

That ain't the problem on the zariman nor does the afk system works like that. A player needs to be flagged as afk every time a mission reward drops. Timing that throughout the whole mission is a nice achievement but doesn't help in this case. And that doesn't explain the missing resource drops and mods (including arcanes). The extraction elevator is more or less known for "stealing" all of your rewards occasionally (i.e. bugs). Happened to me once too tho I didn't do a 2 hour mission beforehand. Best case is messaging the official support and explaining the problem. They helped me too in my case but usually restore only one item. Good luck

As stated in the title. A grineer keeps following Kahl in the Junk Run mission. Happened to me a couple of times and its (when it happens) always the grineer which is in front of the gate leading to Sprag. Command mode works for all grineer (stay at position) but this one. That can interfere with challenges like "kill 10 enemies with grenades" or "kill 5 enemies in 5 seconds" as Kahl cannot gather enemies around him without my follower deleting them first from the mission. https://www.youtube.com/watch?v=rTak84FYH5w Edit: Apparent workaround is letting the unwished follower die in the thumper arena and then completing the challenges. Might take a while as the enemies deal little to zero damage to him

It was a bug (Patch notes: Update 34.0)

Junk run gives you a jetpack from a fallen grineer after the first encounters with the deacons and narmer drones

get out /s

Bugs as such described are not solved via the forums as this is a community exchange between players and sometimes devs. Only the support (https://support.warframe.com/hc/en-us) can help you with missing items.

What sort of bugs?

The empty End of Mission screen is definetly worrysome but after thousands of railjack mission I can assure you don't lose anything provided you leave after the mission rewards pop up.

If the mission rewards pop up at the end of a finished mission everything gathered until that point is saved individually for each player. An individual player may leave the mission after this (via "Abort Mission" even though the mission's completed) and won't lose out on rewards, focus, intrinsics, etc.

Electric hazard prevents teleporting

The description of Lone Story explicitly states that all side objectives are disabled. "Just the Spiral's story. Duviri devoid of all side objectives"

The Maw Fishing counts as a side objective and is therefore not available in Lone Story as it disables all side objectives. You must be in Duviri Experience to be able to do Maw Fishing.

This results from having the riven show the stats for a normal weapon of which also another special variant with different riven dispositions exists, for example Karak and Kuva Karak. The riven stats are first shown for the normal variant while you equip the riven on the special variant, therefore the stats are (in most cases) lower. In the riven reroll screen you can select the weapon variant with the corresponding disposition on the lower right corner just above the image of the weapon.