It looks like the freezes could be a separate problem to the CPU spikes.
Because these look like input freezes:

[ 6939.689860] shallan gnome-shell[15054]: _clutter_stage_queue_event: 
assertion 'CLUTTER_IS_STAGE (stage)' failed
[ 6939.689984] shallan gnome-shell[15054]: clutter_do_event: Event does not 
have a stage: discarding.
[ 6939.699761] shallan gnome-shell[15054]: _clutter_stage_queue_event: 
assertion 'CLUTTER_IS_STAGE (stage)' failed
[ 6939.699930] shallan gnome-shell[15054]: clutter_do_event: Event does not 
have a stage: discarding.
[ 6939.729329] shallan gnome-shell[15054]: _clutter_stage_queue_event: 
assertion 'CLUTTER_IS_STAGE (stage)' failed
[ 6939.729490] shallan gnome-shell[15054]: clutter_do_event: Event does not 
have a stage: discarding.

but I don't know how that could cause high CPU.

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https://bugs.launchpad.net/bugs/1899184

Title:
  CPU spikes and system hangs from gnome-shell every 5-10 seconds

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