Russ Jones from Moz wrote a detailed piece named Google Search Console Reliability: Webmaster Tools on Trial. In short, he said SEOs and webmasters should "remain skeptical of this data," the data provided within Google Search Console.
He then outlined and tested the following five reports:
- HTML Improvements
- Index Status
- Internal Links
- Links to Your Site
- Search Analytics
The most concerning to me was the one most webmasters probably, and rightfully, spend most of their time looking at, the Search Analytics report.
Russ said that Google Search Console only "recorded only 2 impressions out of 84, and absolutely 0 clicks." Here is the chart:
Gary Illyes responded to this criticism in a very diplomatic fashion on Twitter saying "we made sure the SC team knows about it." "Personally I think this is a great post, lots to learn from it," he added.
He did not address and explain why the differences, although I am sure there are. I doubt Google will ever specific point out any reason or explanation of why. It may be a bug in GSC or it may be issues on how they count? I don't know.
Either way - this shows a reason not to just use Google Search Console for data but to also use your own tools or third-party tools.
Forum discussion at Twitter.