I think you will have to agree that a 100MHz scope-bandwidth is only twice the 'frequency of interest', so how could you expect to see anything more than the fundamental, the sine-wave of 50MHz? As the 'sum of odd harmonics', you would need at LEAST the 3rd (150MHz) and 5th (250MHz) harmonics to pass-thru 'relatively undiminished' to start to look square. And working this close to the 'max range', the scope is probably also 'filling in' a sine-wave from the points it CAN read, hence generating a waveform that exceeds the rails. Of course there I am ASSUMING that this 50MHz is NOT driving an unterminated trace, which would of course add its own 'ringing' to the situation! Kinetis silicon is certainly capable of clean, fast edges -- see my 500MHz-scope picture in:
Confirming K22F Clock Frequency
Although not the 'square wave' I expected in that shot, I got said square-wave with 'better code', showing a sequence of 10ns high and low intervals. The point is that signal rise/fall-time can be about 5ns.
1st, 3rd & 5th make 'red' waveform:

Note also how the 'pure sine wave' (green) is at a higher peak-to-peak than the 'final' +/-1 'squared off' wave.