Occasionally, mechs disappear when moving them to/from the inventory window and ready area (the screen before you assign pilots to them). Easily fixed by 'refreshing' - entering and exiting the mech purchasing area. But nonetheless mildly frustrating.
Since there's no more infinite inventory, stackable items would be a huge plus. There is plenty of room on the GUI for this, especially for weapons.
When placing weapons on mechs via drag-and-drop, the inventory window scrolls all the way back to the top every time. This is mildly frustrating when you need to arm a mech with several lasers. Not so bad with PPC's, because they are at the top of the list to begin with.
Inventory is far too limited, and a bit buggy. I went to go buy lasers - turns out, I could only buy one. Even more confusing, the unpurchased items do not remain purchasable in future missions. A maximum of ONE item is purchasable at any given time - and this is supremely frustrating when you want to go build an LRM platform. And why is the per-item-quantity only set to 'one'? Honestly, I'd expect the quantity of those armor plates and heat sinks to go up by a LOT more than 'one' per mission - and likewise for small, bulk-placement weapons (pulse lasers, LRM's, machine guns, maybe light AC's).
The next issue may just be from not playing the game for so long...but all the mechwarriors on my team seem very special in the head. I'm only on the night Liao raid mission, playing on Veteran...and between a heavily armored Bushwacker and five light mechs armed with heavy-hitting ranged weapons, they can just about one-shot-alpha-strike a light mech, and cut up a medium mech in a few seconds. Once I get to the west end of the map, at that base near the end, I blow a hole in the wall with the bushwacker's lasers and heavy AC, charge in, and suddenly all the fire-support mechwarriors go herp-derp on me, and forget that their guns need a clear line of sight. Even after they nuke every segment of the wall now in their way (only after I told them to), they still just walk around like they're either drunk, or playing solitaire on their mechs' consoles.
Also, the resource points are messed up. In all the missions, you start out with 1/10 the normal resource points - so, for example, instead of starting a mission with 7000 (enough for, say, a repair truck), you start out with 700. Which you can't really use...at all.