Playing Eras II as David Mitchell and the big ol Prince of Wales.
Maybe its just because I burn through it too fast but multiple times I've run into a situation where the stores at various ports either had no Powder or barely enough for a single broadside. For example I just checked Port Royal, Fort de France, and that french port on Guadalupe, none of them had powder.

Another issue I've experienced is the complete lack of officers at Taverns. 
I was able to hire 2 officers initially, and then for a bit I'd see officers but the only option was to tell them I had a full crew when I didnt. Now I can't find officers anywhere.  Oh and one of my 2 officers died when the ship I put him in charge of sank so I only have a bosun. 

So those are my two biggest issues, no officers and no powder. I did also have the jewel and moneylender mission bug out on fort du france with no diamond spawning, but thats not a huge game ruining problem like lack of powder. 

EDIT: something else I noticed after starting a Spanish Inquisition run, the third ship in a fleet line always seems to be the one with disease issues. My line has shuffled quite a bit but disease routinely plagues the third ship in line no matter what ship it is.  Why?

Two more things. 

1. I captured an English "102 Gun" 1st Rater, but it only has 100 guns!

2. When I was capturing Rock the Brazilian for the church, I noticed his ship had a max of 30 12lb culverins, and yet somehow he had 24lb ones mounted. 

Stores low on certain cargo has been determined a feature of ERAS and will likely stay as it is.  See a recent discussion here:  https://buccaneersreef.com/forums/topic/anyone-with-issues-of-stores-running-out...

The many other "hero" NPC are traveling around and they actually consume store goods too, so the scarcity is a side-effect of the 140+ hero characters roaming about...COAS had like 4 or so.  MK has determined that this just forces the player to take prizes to compensate.

The scarcity of officers in taverns is also a side-effect as the population of other hero NPCs in town is accounted for during each cycle of tavern patrons.  Even if those NPCs are not always physically in the tavern, I believe it does adjust down the other patrons, and regular officers wind up getting excluded.  I workaround is to ask the other hero NPCs to join you, and if they accept, the you can do what you like with their ship and make them an officer instead.

The English "102 Gun" 1st Rater might be misnamed if it only has 100 guns.  I will have MK review that one.

As for Rock's ship, there are several like that in the game, and it stems from the original COAS.  The Dog of War, Brig Queen, Sea Wolf, and Blue Bird all have higher than allowed cannon calibers; they are just special ships, so I'm assuming that goes for Rock's ship too.