Weird note structure on guitar audio waveform
Here are some possibilities:

Transverse waves on a guitar string have two polarized components, one parallel and one perpendicular to the guitar's soundboard. User hotpaw2 mentioned energy exchange. It is imaginable that energy transfer could happen between the components. The component parallel to the soundboard is largely inaudible, so it could stealthily store energy until released later.

Or it could be that you have two strings with modes that are slightly out of tune, and they form a beat frequency.

EDIT: Having analyzed the audio sample, the things you have marked are just some low-frequency artifacts, I think from things like someone touching or shaking the mic or moving around and bumping the guitar body. Adding a 100 Hz high-pass filter mostly gets rid of those:

Figure 1. Sample after 100 Hz highpass filtering.