Membership type is setup so that when assigned to an organization, the employees of that organization also inherit the membership.
Problem: Not only is the membership getting passed down, but also the contribution if recorded through the membership form.
So if ACME Company becomes a member and pays $200, all employees of ACME Company have a membership record (good) but also a contribution record for the $200 payment (very bad). That's problematic because it basically throws all contribution records/searches off.
The following demo data is identical on both 2.0 and 2.1 sandboxes:
Membership org = Demo Membership Org
Company = ACME Company
Employee = John Doe
Employee = Jane Doe
Membership Type = Indiv inherits Org
Membership + Payment is assigned to ACME Company. In 2.0 sandbox, both membership and contribution inherit. In 2.1 sandbox, no inheritance takes place (seems to be broken).