Order number suffixing and sequencing
When you edit an order, by default, Edit Order will append a suffix to the order number for the new version of the order to indicate that this is latest version of the order. For example, if you edit Order #1001, Edit Order will create Order #1001A with your updates.
Because of the way Shopify works under the hood, this can give the impression that orders are not being created in sequential order.
The good news is that this is a normal (albeit, confusing) behavior of Shopify when an order is edited and does not represent any orders that went missing. Though we can't stop Shopify from incrementing their internal counter, fortunately, we haven't heard of any merchants about issues that this causes, especially once they get used to it.