Lumps after Carpet Stretching
Your guess about the padding bunching up in highly possible. If the carpet was installed over the pad for some time it may have stuck to the padding in some places leading to the padding being pulled out of position as the carpet was restretched. There are a number of things that could cause carpet to pad adhesion.


A carpet backing material inherently incompatible with the type of padding.
Environmental conditions that cause the padding to decompose into a sticky goo that pastes to the carpet backing.
Hot melt carpet splicing tape where some of the glue oozes out from the edges of the tape and adheres to the padding.
Something was spilled on the carpet at one time that bled through the backing and made a sticky mess at the padding but was unable to be fully cleaned from above. Think 'can of soda' or similar.
Heavy furniture with legs that caused high pressure point locations that compressed the carpet and padding so tight together over a long period of time that they literally bond together.