Why a Merged PDF Came Out With Pages in the Wrong Order
The most common cause is assuming files will be merged in filename or alphabetical order when the tool actually merges them in the order they were added or selected — a second common cause is not accounting for the fact that a multi-page source file contributes all of its pages together as a block, not interleaved with other files' pages.
This is almost always a mismatch between an assumed ordering rule and the tool's actual, simpler behavior, rather than a bug.
Upload order vs. assumed filename order
Most merge tools combine files strictly in the order they were selected or added to the tool, regardless of filename — assuming a tool will sort files alphabetically or numerically by filename is a common but often incorrect assumption, and checking the tool's actual order (and reordering manually if needed) before merging avoids this mismatch.
Multi-page source files contributing as a block
If one of the source files itself contains multiple pages, all of its pages are inserted together as a contiguous block wherever that file falls in the merge order — they aren't interleaved with pages from other source files, which can produce an unexpected structure if the intent was actually to interleave pages from different documents.
How to verify order before finalizing
Checking a preview of the file order (if the tool offers one) before completing the merge, or opening the final merged file immediately afterward to confirm page order, catches an ordering mistake before the file is distributed or submitted somewhere it matters.