The system is allowing a picking list to be created for only a portion of the bundle lines. For example if the bundle contains 4 lines but only 3 of the 4 lines have on hand inventory. When generating a picking list using the "Reduce quantity" slider it only allows picking lines for on hand inventory. Three of the lines get a picking list created and the 4th does not.

Once stock arrives for the remaining bundle line, system is not allowing the generation of the additional picking list so the remaining bundle line cannot be picked, shipped and invoiced together with the rest. 

The same is happening when using advanced warehouse release to warehouse functionality. The system is allowing lines that can be reserved to be released to warehouse and preventing remaining line to be released once stock arrives.

The only way to fix the orders is to disable the Revenue Recognition feature, adjust the orders so you can process them through, then re-enable the feature. Microsoft indicated a customization is needed to prevent this. This should be standard functionality of bundles that they are never released separately. Please vote for this feature before you too have stranded orders in your system.