Problem

The way git works when it comes to file history is that entries returned are likely to be simplified, so that changes that even each other out are not displayed. As from the git documentation:

Simplifies the history to the simplest history explaining the final state of the tree. Simplest because it prunes some side branches if the end result is the same (i.e. merging branches with the same content)

Bitbucket Server relies on the default git behavior concerning history simplification, resulting in some history entries being omitted when looking at file history. A possible scenario, when you modify a file in a commit, then afterwards merge a branch that has the earlier version of the same file. In such a case, neither the original commit, nor the merge commit are shown in the file's history, as the sum of the changes results in the same file.

Workaround

To see the complete history of the file, use the following command in the git repository on disk, using git command line client:
git log --full-history --graph – <path-to-file>

Suggestion

Provide an option to see the "full history" of files in some way. Possible solutions may include, providing this as a per-user, per-repository or per-project setting or simply have a Show full history button when viewing file history. An indication of omitted history entries would be beneficial in that case.