Every facility has a quality level (I, II or III), which is shown after the facility's name, either in its window or its icon tooltip on the main menu. That marker defines the development level of the facility: level I has a relatively high cost of operation, level III quite a low cost of operation. Search for the most economical solution by traveling between terminals!
It's fairly common that an item, especially looted ones get damaged. You can fix them (or the bots that use them) in any Repair shop.
The repair shop automatically sorts out damaged items from your private storage, so you only need to choose the items you actually want to repair – no sorting through items in good shape. Then just click on the repair button. Repairing an item will cost you a certain amount of money, but that amount can be cut down by improving certain ratios, specified below.
Repairing bots in station tends to be an expense that can be avoided –just deploy with an armor repairer fit and run it. There are situations where this isn’t possible, but in general, you can save money by doing so.
Additional parameters that affect your total efficiency.
Relation ratio - Improve this factor by reaching a good relationship with the owner of the facility.
Discount ratio - Cheaper repairs can be had by training the Basic Repair Technologies extension.