In the settings tab you can change some of the behaviour of the app.
When you manually start an activity in Google Fit, or if you enter the activity afterwards, Google Fit creates what is called a Session. This session is visible in the Journal section of the Google Fit app. Also, if a third party app stores the activity it is usually stores as a Session as well.
When counting activities for a frequency goal the default is to count the number of sessions of that activity. This will normally work for all activities.
However, for walking and running activities Google might also auto-detect such activities. If the activity is long enough, or if there many activities of the same type close to each other in time, it will show up as an entry in the Journal section.
These auto-detected activities are not stored as Sessions (even though they are visible in the Journal section in the Google Fit app). Because of this they will not be counted towards the frequency goal.
If you want to count also auto-detected walking or running activties towards a frequency goal you can try to change the data source to Segments instead. This will count the number of uninterrupted periods of activities instead of counting Sessions.
As mentioned above, to be visible in the Google Fit app the segment has to be long enough. Also, if there are multiple segments close in time they might show up as one entry in the Google Fit app
Google has not published what algorithm it uses for an auto-detected walking or running activity to be visible in the Journal section in the Google Fit app. Fit Companion will try its best to mimic the behaviour of the Google Fit app, but you can try tweaking the below 2 parameters if you see that the frequency count of auto-detected walking or running activities are not the same as in the Google Fit app.