Explanation of fundamental filtering's consequences on signal
As already mentioned by @Fat32 in the comments to your question what you're observing is not commonly referred to as overshoot.

As there are no units on both plots comparing the results in both figures is somewhat difficult. The following assumes that the horizontal axes in both plots are just the indices of either the time or frequency domain values (otherwise the graphs cannot be directly related without additional information and/or do not make sense).

The exact effects of what you're observing will generally depend on the frequency, amplitude and relative phase of the harmonics present in your signal.

A rough visual comparison of the green and blue lines in the first plot indicates that indeed the first harmonic has been removed. The difference between the green and blue lines is roughly a sine wave (phase zero) that fits into the window (i.e. no difference at the start, end and 1/2 of the window; largest difference at roughly 1/4 and 3/4 of the window). 

Note that if the amplitude and/or phase of the first harmonic are different the time domain signal, resulting after subtraction of the first harmonic, will probably look completely different.