Clock Shape Changes with Two O-Scope Probes
The waveform isn't square as your scope only has 50MHz of bandwidth.

A 10MHz square wave has significant frequency content at well above that.  All you are seeing is the result of low-pass filtering at ~50MHz which means you are only getting the fundamental and a couple (at most) of the odd-harmonics.

Why is changes with two probes is also similar - you are adding more capacitance across the signal, which also acts as a low-pass filter.  You may also be loading the oscillator more than it can drive "nicely".  Check the impedance of the probes.