I love this game, it's so well crafted with so many details for exploration, the atmosphere is just awesome. But there are some minor things that I found really annoying and frustrating during the gameplay. 

I hope this will be red by the developers and maybe they can take a look at those details in the future :-)

Using numbers to choose items actions
When I open my inventory a select some item, I can for example just press "5" in order to start holding the item. However when I hover item on the ground, I need to press the number and then press "E" to activate the action. This is such a minor detail but so frustrating when working with a lot of small items on the ground! The useful way would be "just press the number and it's done!"

Inventory items order
There are arrows "up" and "down" in the inventory which does nothing. I would like to setup my inventory so my favorite tools are always at the same place! But I can't easily do it. This is also related to that the new items added to the inventory appears usually as the first item, shifting all other items back - but not always (confusing). The most useful way would be "new items to the end of inventory".

Putting items into boxes / backpack / bin
Currently when I hold a box and want to put an items from the ground into a it and then transfer the full box somewhere else, I need to: 

1. Put the box on the ground. 
2. Click on the item on the ground and put it into my inventory. 
3. Click on the box on the ground and "use" it. 
4. Transfer items from the inventory into the box. 
5. Hold the box so I can transfer it elsewhere.

This is so frustrating when e.g. cleaning the base. I wish there could be better way like: "Hold the box → left click on the item on the ground → it's inside the box now!". 

Controlling Kerfur through the camera
When Kerfur gets stuck somewhere, I know I can press "back" button on the camera screen and then control the Kerfur manually. It just feels it's not working properly. I can only shift Kerfur to the side a little, but it is still trying to go forward so at the end this way is very frustrating and in reality not working most of the time. I've found myself not even trying anymore and just let Kerfur die out of battery (and then come to grab him the next day).

 
Feel free to add your own "annoying details" of the game :-)

Absolutely agree with everything. I have since gotten used to some of the controls, but I adapted to work around the frustration.