This is really sort of misleading, because a district in which Trump did not get the majority is not the same thing as a district that Clinton won. Some of these districts were districts with a vote total like 48% Trump, 45% Clinton, 7% Third Party. If there had not been any third party candidates on the ballot, and the vote shares for Clinton and Trump had to add up to 100%, then Trump would have won majorities in some of those sorts of districts.
A district like that is much harder for a Democratic congressional candidate to win than a district that is something like 48% Trump, 52% Clinton, even though in both districts Trump has 48% (less than a 'majority').