How did you create the shape? Without seeing the modified properties of the layer that is giving you the problem it's almost impossible to tell what's going on. There is no reset bounding box in After Effects, but a more efficient technique in creating the shape in the first place may give you what you need.
To show the modified properties of a layer press the U key twice. To give us screenshots that are useful in diagnosing problems please use Print Screen or Shift+Ctrl/Cmnd+3 on a Mac to capture the whole AE interface making sure that anything that may be causing problems like the footage info or the comp that is displayed in the Project Panel is selected and visible as well as the modified properties of the layers giving you problems is visible, then paste or drag the screenshot from the desktop to the reply field on this forum so we can give you some better suggestions.
Thank you for your help. It was an imported shape from Illustrator – which was already rotate there, so when imported to AE, it gained the bounding box which was not aligned to its rectangliness. I imported the original shape levelled to 0° and that worked well. Is there no other way to change bounding box orientation if I'd really need to in the future without recreating/reimporting of the shape?
Maybe can I somehow export the vector, rotate it in AI and then import back?