No, there cannot be pathological bit patterns in Manchester encoding. It can handle over 10,000 consecutive bits of consecutive 1's, 0's, alternating, or any other pattern. That is why it was chosen for disk drives over 30 years ago. It got eclipsed by FM. MFM, MMFM, RLL, GZR, and other techniques about 20 years ago that achieved higher bit rates with equal flux change rates (especially for the last three).