It really is necessary to take a look at your current system to get to the bottom of it, but one possible issue is duped conversion data. An example of this would be tracking Facebook ads, Google Adwords and organic conversions, tracking these out of the platforms themselves you may have them all reporting a conversion at the platform side. If you compare this to a de-duped view either through attribution modelling out of GA or another view, then you would get a different picture of CPA.
It becomes more difficult as you start to use display and remarketing advertising as well, so these may be factors at play.
The other option is just the way the tracking is fired, GA will have variance to Adwords, to DoubleClick etc. even though they are all Google platforms, it's just the way it is.
As with all things tracking, it's about understanding there will be variance, but putting in place measures to reduce it, we call it "being less wrong". At the moment you have +/- 100% which is obviously not acceptable, but a few measures in place to get one source of truth with +/- 10% would probably be completely acceptable.
Happy to schedule a call if you'd like to discuss this in more details.