When collecting a void spot fills your reactor to capacity, the remainder is wasted -- this makes it take ages to purchase upgrades that have costs very close to your maximum capacity, when the only way to really get that close is through void spots.
In the idle game Machinery, there's a very similar concept with the generators going "overcharge" and dumping a huge pile of energy all at once. However, if that energy exceeds your storage capacity (and it usually does), the excess is buffered for a few seconds, giving you a chance to buy all the upgrades possible with the amount of energy.