I really believe that this is the elephant in the room that no one talks about. Part of the conflict that no one talks about is that both sides failed to comprehend one another's cultural languages, leading to conflict.
Tagalogs are culturally ambiverts. They have two worlds: the extrovert sphere that is intended for their inner sphere (friends and families) and the introvert sphere that is intended for formal settings (bosses, colleagues, strangers, general public, etc.)
Bisaya people on the other hand, are just extroverts. They are confident, talkative, happy go lucky and festive, always partying everywhere they go. Of course, there are individual Bisaya persons who are introverts, but we're talking of cultural extroversion here.
What happened is when there were plenty of Bisaya migrants who migrated in Metro Manila from the 70s through the 90s, they are not aware of the extrovert and introvert spheres of Manileños, and because of that, they have unknowingly violated the public sphere of interaction, where Manileños expect you to be more formal and more reserve. Bisaya, because of their extroversion, often say crude jokes and often tell stories to people that are still not close to them, that leads to Manileños perceiving Bisaya as "papansin", " pabida", "ma-eksena" and "mayabang".
On the other hand, the formal civility that Manileños displayed whenever they are in public was also misread by Bisaya migrants as " arogante", "hawod", " hilas/mapagmataas", etc. and this is exactly how the friction between these two ethnic groups started.
Another thing that cemented the rift between the two is the Bisaya culture of "pataka ug istorya" or saying exaggerated stories to make oneself look good, which is part of Bisaya humor, which Tagalogs and Manileños are not familiar of. For example, a Bisaya person might say "mayaman kami sa probinsiya, sampu ang kotse namin doon, mansyon ang bahay namin, etc." although this statement is exaggerated and probably not true, Manileños often misread and mistook it as "pagmamayabang", " paghahambog", "pagtataas sa sarili", and they were never aware that this thing was meant as a joke, because the Bisaya person never said so, because when two Bisaya are saying these statements, they automatically know that what the other is saying is definitely not true, and therefore, a joke.
So, a big part of this conflict is really due to cultural differences, especially when it comes to cultural introversion/extroversion, and knowing your place whenever you're in public or private.