If your store uses Shopify Shop Promises and post-purchase items are being shipped separately from the original order, this is because post-purchase upsells are not supported by Shop Promises.
Affected Orders
Orders that are covered by the Shop Promise Guarantee will be affected by this issue.
You can identify if an order is covered by a Shop Promise by viewing the order in the Orders tab of your store's admin console and looking for two things:
The Shop Promise logo on the shipping information
A message in the timeline notifying you that the order is covered by a Shop Promise Guarantee