I am getting to the mid- late-game now and I have really started to notice issues with transferring items between bases. There seems to be a maximum quantity each item that you can transfer at one time.
e.g. I tried to transfer all my Alien Materials to one base to build a ship, (6+ Harvesters worth of materials for 1 fighter?) but I could only transfer them in batches of 10. That makes transferring 5000 materials really tough. I got around it by selling it all, then buying it all back at the destination, but even then, with no repeat on the quantity spinner, holding shift to transfer 2 with each click instead of 1, it took 500 clicks for 1000 materials to sell, then another 500 clicks to buy it again. I assume that will be fixed by changing the spinners in the buy/sell screen, but I believe different buy/sell prices for items in the market is on the near horizon so that would be expensive.
Some items you can only transfer one of at a time, like ship components. I think I could transfer 3 grenades at a time. It seems to change depending on which base you start at and go to as well. It is just odd and I'm not sure what the purpose of it is, if any.
Might be this:
http://sourceforge.net/p/ufoai/bugs/3406/