The format PDF allows to append changes to a PDF without touching the original bytes of the former document revision. These appended changes are called incremental updates.
If you apply that mechanism to a signed PDF file, the signature mathematically remains valid because the original bytes remain the same. This is why PDFBox outputs that the signature is ok. For details see this old answer.
Of course signatures that remain valid after arbitrary manipulations are not helpful. Thus, only certain changes are allowed in incremental updates to signed PDFs, see this old answer.
Analyzing the changes is non-trivial. Also, the allowed changes are technically not well-specified. Thus, PDFBox has not implemented a check whether incremental updates to a signed PDF are allowed, its example validation code merely outputs if there are incremental updates after the signature or not.
Adobe Acrobat, on the other hand, has implemented a check of the incremental updates. Due to the mentioned deficits in the specification of the allowed changes, though, this implementation has changed quite a bit in the recent years. There are still multiple false positives and false negatives in its reports, though.
In the case at hand, therefore, the PDFBox example class ShowSignature
outputs something along the lines of "Signature valid, but there are changes in incremental updates", Adobe Acrobat indicates a broken signature (due to the changes in the incremental update). Both are right in their way.