Accepted answer
At room temperature it can show up as either, and which one depends entirely on whether the product still elutes under the main peak. Purity is a ratio of areas, so a degradant only costs purity if the method resolves it. Content is a mass against a standard, so a degradant costs content whenever the parent is consumed — resolved or not. Two chains join, usually through a disulfide, so the product is roughly twice the mass and shows up as a late peak — or as nothing, if it never comes off the column. That is why the two measurements are not interchangeable and why an unchanged purity figure after an excursion to room temperature is weak evidence: the method may simply be integrating the degradant along with the parent and reporting the sum as one peak.
This is answerable from the chemistry rather than from anecdote, which is unusual and welcome.
Aggregation is physical: peptides unfold at air-liquid interfaces and associate. Shaking maximises that interface, which is why swirling and shaking produce visibly different outcomes on the same vial.
Put another way, deamidation converts asparagine or glutamine to the corresponding acid via a succinimide intermediate, adding one dalton. It is base-catalysed, accelerates above neutral pH and is the dominant aqueous pathway for many peptides.
Aggregation at air-liquid interfaces is established from surface-tension and particle-count studies and is the basis for anti-agitation handling guidance.
Swirl, never shake. Aggregation is a handling problem more than a time problem.