Different questions and suggestions.
First, an attempt to solve the problem in the acquisition:
1) Overload: It looks like the sine tone you are acquiring is extremelly overloaded (it clips at 10 Volt). This could be disturbing your measurement. Can you by any way avoid this overload?
2) cross-talk between channels: you are running your board at a scan-rate of 200 kHz. This is over the specifications of the settling time of the board. Try to decrease your scan rate and see if this fixes your problem (or at least reduces it).
3) Is the problem still there if you only acquire channel 1? If yes, the problem is not cause by scanning issues but most likely be due to bad connectivity, grounding issues, common mode problems, single-end / Differential co
nnection. This depends on the way your signals are connected.
Removing the problem in post-processing:
4) if everything else fails, you can remove the sine tone from your "spike signal" as follow: On the sub-VI "Extract Single Tone Information.vi" create a constant "Residual signal" for the control "Export signal". The time signal exported (on top of the VI) will then be what you are looking for, that is your signal with the detected 50 Hz sine tone removed.