A good example of one is when you are cloaked and a NPC and or any click-able window comes up and you click it or collect an item your ship will de-cloak.
Sorry, but this appears to be working as intended. Seen here in the Ask Cryptic:
Q: (tovalmorgan) Are you ever going to fix the decloaking bug? Whenever your bridge officers talk to you or any kind of interaction window pops up on the screen while you are cloaked, the pop up window forces your ship to decloak.
Dstahl: To clear up some confusion about this issue, let me shed some light on how cloak is intended to relate to interactions within the game. It is our intention that any interaction within the game will remove stealth. Anytime you are expected to take a game action of clicking on a button to respond, whether it is to scan something, or acknowledge a bridge officer, or make a command decision via a contact option, it should pull you out of stealth. With that said, there are undoubtedly missions out there that were made prior to the inception of the mini-contacts (the ones that fly across your screen) which are just providing information and shouldn?t need to be acknowledged. One reason we created mini-contacts was to allow information to be given by your bridge crew without you needing to acknowledge it for game design purposes. If you feel that a specific mission contact could be switched to a mini-contact that doesn?t need acknowledgement, then that is the type of suggestion that should be made. We can then look at the mission specifically and determine whether it warrants a mini-contact or not.