Why is there a difference in numbers between Google Analytics and Website Analytics in Marketing Automation?

Why is there a difference in numbers between Google Analytics and Website Analytics in Marketing Automation?

Zoho Marketing Automation is not an alternative to Google Analytics. 
Both follow a different method of tracking visitor's data and their behavior on your website, so you can't directly compare the data collected in Marketing Automation with Google Analytics. Below are a few of the major differences you will see between Zoho Marketing Automation and Google Analytics in tracking your website metrics:

In Marketing Automation, visitor metrics are collected based on Unique Visitors, while in Google Analytics, visitor metrics are collected based on Sessions.

Here, a Unique Visitor means a person who has visited your website at least once (first time visitor) and is counted only once in your experiment report. This means that regardless of the number of times the same visitor comes to your site and the number of different experiments they are part of in a given month, that visitor will still be counted as one.

Alternatively, a Session in Google Analytics refers to the set of actions or interactions of a user (both new and returning visitor) on your website in a given time period. In other words, a Session measures the volume of visits to your website. For example, a single session can contain multiple page views, events, and ecommerce transactions. By default, a Session will expire after 30 minutes of user inactivity.

For example:
Let's say a visitor enters your website and performs a few clicks or interactions on a page. In GA, this visitor interaction will be counted as a new session, say 'Session 01', and the corresponding visitor be recorded as 'Visitor A.' If the same visitor re-enters your site after 30 minutes of inactivity on your site, then the previous session (i.e. Session 1) will expire, and a new session, say 'Session 2', will begin and start counting that returning visitor as 'Visitor B.'
In Marketing Automation, the same visitor is counted only once, regardless of whether they are new or returning to your site, unless they clear their cookies from their web browser.
Google Analytics takes a minimum of 24-48 hours to update custom variable data in your report, whereas Zoho Marketing Automation reports your experiment's data in real-time.