I have set up a flat rate of $12 for all my products online, any orders over $100 customers receive free shipping. For some reason with a particular bundle of products one customer ordered, the flat rate automatically charged a standard fee of $20.95 with in brackets (-$12 for orders over $100). The total order for the customer was worth over $140, I cant understand why this flate rate of $20.95 is popping up at checkout when it was never created in the first place!
You have conflicting shipping rules most likely. Shopify lets you set a bunch of different properties for each item if you wanted, for each district, with a bunch of variables. That particular item is probably toggling the fee on multiple shipping categories causing them to stack up. If you go through your shipping settings tab you'll probably find the problem (also check the product in question, your weight/value could be causing the issue too).
One of the early struggles of being on shopify is getting all your backend stuff sorted out and working nicely lol. But once thats done you can more or less forget it and just let it keep working on its own.