You might be accidentally drawing with the Pen or Pencil with non-regular settings. When you see it happen, check the control bar of whichever tool you're using. Make sure the Shape option is set for None.
Whenever you see it happen, pause for a while, check the status bar, try to find some more clues. We commonly see complaints about not being able to see a stroke, and the cause is usually either the user had turned off the stroke and forgot, or they made it transparent accidentally. Here's a small article/tutorial to help you fix any transparency or opacity issues you might have:
https://forum.inkscapecommunity.com/ind ... article=18