Spotlight Concerns?
 

I cloned my internal drive to a volume on my external hard drive. Before the clone I disabled spotlight indexing of the external drive.

I just started a clone of the external hard drive to the internal drive and realized that I never disabled spotlight of the internal drive once I booted from the external drive.

This means that right now while it is cloning, spotlight is probably trying to index the drive that SD is cloning to. Is this a problem? Will spotlights indexing effect the integrity of the clone?

No, it'll be fine.