The U.S. Conference of Catholic Bishops explain the issue succinctly here:

In line with longstanding federal jurisprudence, the authorizing legislation for Community Health Centers creates a presumptive mandate for funding abortions without meaningful limit. Currently such funding is prevented only by the fact that funds under the Labor/HHS appropriations act are governed by the Hyde amendment. By appropriating new funds not covered by Hyde, and by failing to include any relevant abortion limitation of its own, the Senate health care bill as presently worded would disburse billions of dollars in federal funding that no one could prevent from being used for elective abortions.