95 oldsmobile 88 3.8 fuel lines
 

When I was repairing nylon fuel line return line (3/8) sticking the hose in hot water (to go over barbs) created bubbles in the water. Does this mean I could have possibly got water in the lines?

Possibly.

My suggestion: Get a big zip-loc bag, stick the end that you're trying to warm up in the bag, put the bag in the warm water such that no water gets inside the bag or hose, voila'.

Hair dryer or heat gun will work also.