UPDATE - Spoke to the LBS he said there was a puncture caused by a big ol thorn. He added that he took a photo of it.
So ermmm apparently that was it.... Wonder if any LBS's purposely insert a thorn or nail to make it seem like there was a puncture when there wasn't? Not saying he did that. Just something I thought of. It would be VERY easy to do that after all.
You're overthinking it. Trail and track riding (even on the roads) thorns and flint shards are a common problem so no surprise the LBS found one.
One important thing when you're learning to fix punctures, as the tyre is off, run your finger around the inside of the tyre itself, feel for thorns, spikes, shards etc. Nothing worse than fixing a puncture then it immediately deflates because you didnt take out the (unseen) offending thorn/glass/ shard. A fingertip is very good because its sensitive, but go gentle so's not to injure yourself
At the end of the day, you have several options that will help prevent punctures but not completely.
Buy better tyres.. puncture resist tyres have better protection but tend to be heavier
Buy some slime and use that. It does generally work but it adds weight
Plus tyre liners etc etc
You pays your money, its pros and cons with each option.