This is pretty brief/general, but it's the paragraph from the PC description of BPD that relates most to mood issues in BPD (the types of things that can either be confused with -or- overlap with bipolar:

Individuals with Borderline Personality Disorder may display affective instability that is due to a marked reactivity of mood (e.g., intense episodic dysphoria, irritability, or anxiety usually lasting a few hours and only rarely more than a few days). The basic dysphoric mood of those with Borderline Personality Disorder is often disrupted by periods of anger, panic, or despair and is rarely relieved by periods of well-being or satisfaction. These episodes may reflect the individual’s extreme reactivity to interpersonal stresses.

I can see how the irritability and anxiety cited above could be confused with a form of hypomania or mixed episode. It must be hard for pdocs to make these distinctions, but I guess they have their ways. I think there are a lot of different things (perhaps not encompassed in any one article) that are taken into account. But along with distinguishing between the two, obviously both can exist simultaneously, where as someone here wrote once, the one just feels completely different than the other -in other words, the day to day stuff feels completely different, is a completely different experience, than an episode.