In a second, a power supply applied to lithium cells probably wouldn't damage them. The cells would damage the supply if backwards.
I think resistance through incorrectly biased transistors and capacitors would be high enough the cells wouldn't see a direct short, rather would deliver a tolerable couple hundred amps at most.
New supply connected correctly, if it charged cells higher than 3.6V and stayed for days, that would cause damage.
If only applying 3.3V indefinitely, shouldn't be any damage. Still 3.3V would indicate hasn't hit knee of curve.
"Swelled" - as has been asked, swelled how much? Some swelling reportedly occurs during charging.
People often clamp to prevent slight welling, because vendors indicate that extends life.
How much current was flowing during charging?
What voltage was supply set to?