Unsure what some of the sounds mean during a quest

What is that little "high pitched ding" that sometimes plays during a quest? Is it PSE related? It has no popup or anything and to clarify I'm not talking about dark blast/photon blast charge.

Another thing, what does it mean when the heartbeat sound plays and the screen darkens red? Is that related to the D-factor from story mode, or does it actually mean something?

Those are "Omens"; basically, they mean that a specific kind of E-Code has high chance of happening or that a special event has occurred, but it may not occur if you don't pass by the necessary spawn point. I'm not sure what the first one is exactly (it just might be the one that indicates a red container has spawned), but the second one is related to Falspawn-based E-Codes.

The omens are meant to tell you that the next PSE Trigger (When killing an enemy) has a higher chance of causing that PSE effect to occur.

There's also some visual effects that occur, which I've described here: https://forum.pso2.com/topic/5786/in-mission-sound-and-visual-events/2

Some times the "Ping" could be a hidden mine going off, most classes can't see them, but Rangers have a passive to spot those a head of time, there are random chances one of these mines might inside a crate you smash though.

I run a ranger and when I see a mine activate, it also makes a distinctive ping sound.

The high pitched sound with no visual you are describing is probably the red container spawned somewhere on the map indicator. (Not to be confused with rare drop red box.)

Thanks for the replies!