Hi @kinnera ,
This could happen due to two different visitorsID generated one for domain A and another on domain B. The visitorID is generated using the Adobe OrgID. Can you check if both DomainA and DomainB impmetations use same Adobe ORGIDs/instances?
Also you mentioned activites are mapped to direct traffic source. This can be fixed by defining Internal URL filters in Analytics reprotsuite general settings also fixing Marketing Channel Processing Rules.