Several files or scans need to become one document.
Why your merged document came out in the wrong order
Merging is simple until page 10 lands between page 1 and page 2. That is almost always a sorting problem, not a tool problem.
The reason 10 comes before 2
Most systems sort filenames as text, character by character. In text order "scan-10" comes before "scan-2", because the character "1" comes before "2". The scanner did nothing wrong and neither did you.
Padding the numbers fixes it permanently: scan-01, scan-02 … scan-10. From then on text order and page order agree, in every tool you ever use.
Check the order before you merge, not after
Confirm the sequence while the files are still separate. Reordering pages after a merge is possible, but it is slower and easier to get subtly wrong in a long document.
If pages came from a phone, look for duplicates before merging. Photographing a stack usually produces at least one page captured twice.
Rotation is separate from order
A page fed in sideways stays sideways through a merge. Rotate it first, or the finished document will be correct in sequence and unreadable in practice.
Rotation applies per page, so a document with one landscape table among portrait pages can keep the table landscape deliberately.
Photos are a different starting point
Images have to become PDF pages before they can be merged like pages. Converting them first also lets you set the page order and orientation once, instead of fighting it later.
Photographed pages also arrive at inconsistent sizes, because the camera distance changed between shots. Pages that vary in dimensions look ragged once bound into one document, so it is worth normalising them before the merge rather than explaining it afterwards.
Two-sided documents scanned in two passes
A duplex stack run through a single-sided feeder produces all the fronts, then all the backs — and the backs usually come out in reverse order, because the stack was flipped.
Merging those two files end to end gives you every front followed by every back, which is not the document. The pages have to be interleaved, and the reversed half re-sequenced first.
Check page two of the result immediately. If page two is the back of the last sheet rather than the back of the first, the interleave went in the wrong direction and every subsequent page is wrong too.
Before you send it, read the seams
Look at the join between each source file rather than skimming the whole document. That is where a duplicate page, a missing page, or a sudden change of orientation shows up.
Confirm the final page count against what you expected. A merge that silently dropped a file is much easier to catch now than after the document has been signed.