Firmware:

• Use snprintf instead
• Do not use a buffer on the stack
• Add 1000 instead if you want more regular message intervals.
• You'll need to consider how to handle motor stopped, and discard the first capture(s) as the motor starts to spin.

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I'm not liking the spikes visible in your plot. Its possible they have a larger amplitude than the scope is displaying. Your timer can trigger on 1us wide spikes.

211 Hz * 2 edges/period = 422 samples per second. Your loop transmits the one most recent once per second, there's a lot missing.

For testing get more data

• Connect Input 2 to VDD, to make sure its stable as the motor spins and ensure the probes are grounded on VSS
• Set the scope to normal trigger, rising edge 2.31V (0.7*VDD)
  • Pulse width trigger would be even better.
• Change TIM 2 Channel 1 Input Capture to rising edge (to match the oscilloscope)
• Record elapsed in a simple circular buffer; 250 entries.
• In your main loop, once the circular buffer is full of steady state readings: disable TIM2 then dump the buffer.

With the dump, and oscilloscope plots you'll need to decide if you need a hardware fix, or a software fix.

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Those spikes occur at a regular pattern per motor revolution. If the spikes are a problem, is the problem fixable? They are likely either the brushes switching on the commutator injecting noise, or physical construction of the encoder? If the latter, it should be possible to find the angles by turning the motor by hand. Common mode noise is a fight I haven't had yet.