Is there a "not equal" in a linq join

No, a "not equal" operator would get you all combinations of groupA and groupB except the ones where the items were the same.

Using the Except method gets you what you want:

var filteredEmployees = groupA.Except(groupB);

You don't need a join for that:

var filteredEmployees = groupA.Except(groupB);

Note that this will be a sequence of unique employees - so if there are any duplicates in groupA, they will only appear once in filteredEmployees. Of course, it also assumes you've got a reasonable equality comparer¹. If you need to go specifically on name, you can use ExceptBy from MoreLINQ:

var filteredEmployees = groupA.ExceptBy(groupB, employee => employee.Name);

Or without going into a third party library:

var groupBNames = new HashSet<string>(groupB.Select(x => x.Name));
var filteredEmployees = groupA.Where(x => !groupBNames.Contains(x.Name));

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¹ As pointed out in the comments, you can pass in an IEqualityComparer<T> as an argument to Except. I have a ProjectionEqualityComparer class in MiscUtil which makes it easy to build a comparer of the kind you need:

// I can't remember the exact method name, but it's like this :)
var comparer = ProjectionEqualityComparer<Employee>.Create(x => x.Name);
var filteredEmployees = groupA.Except(groupB, comparer);