After over a decade of reading medical school and residency letters of recommendation (LOR), I can tell you that the biggest error I see in the LOR process occurs when applicants settle for mediocre letters. In other words, they know that a supervisor/faculty member/attending isn't going to write them a strong letter, but they fill the LOR slot with the middling endorsement anyway.
Please take a look at my most recent Student Doctor Network article, "Get a Better Letter" for concrete ideas on how to approach the letter of recommendation process.