The following is an example of this bug by a very small session, after having removed ~/.gnuplot_history before starting gnuplot. I have added my own numbering of the commands.
--------------------
1: gnuplot> a=5;plot x
2: gnuplot> plot x
3: gnuplot> history
    1  history
4: gnuplot> plot x
5: gnuplot> plot x
6: gnuplot> plot 2*x
7: gnuplot> history
    1  history
    2  plot 2*x
    3  history
8: gnuplot> plot x
9: gnuplot> q
--------------------

Command #1 was typed as is.

Command #2 was obtained by up-arrow, 6*left-arrow, 4*rubout, enter.

Command #3 was typed as is; before typing, up-arrow recall showed me command #1 and not #2. But neither are in the history (file).

Command #4 was typed as is; recall before typing showed #3 and #1, not #2.

Command #5 was typed as is; recall before typing shows #3 and #1, not #2 or #4.

Command #6 was typed as is; recall before typing shows #3 and #1, not #2, #4 or #5.

Command #7 was typed as is; recall before typing shows #6, #3 and #1, not #2, #4 or #5.

Command #8 was typed as is; recall before typing shows #7, #6, #3 and #1, not #2, #4 or #5.

Command #9 was typed as is; recall before typing shows #7, #6, #3 and #1, not #2, #4, #5 or #8.


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