Anyone know why a Work Order Completion would be generated at an early step, prior to all other steps being finished in a Work Order?

If by generated, you mean something automatically happened, then there must be some customizations in your account. For one, you could do them in the correct order (WO > WOI > WOC), and then delete the WO Issue, to recreate it at a later date-time in Netsuite. GL entries will get messed up...