When the team finds Molly, she has only had benzodiazepines, not opiates, and the team knows this. Emily gives her a shot of naloxone anyway to undo the drugs and wake her up, but naloxone only works for opiates. It doesn't reverse the drugs she's already taken and wouldn't wake her up.
Bonnie Sullivan's brother says the only drug his sister did was methamphetamine, and she only smoked it. Yet earlier in the episode she stated that while in rehab she was given Suboxone to help her detox. Suboxone is one of the brand names for the semi-synthetic opioid called buprenorphine, in the form of Suboxone the buprenorphine is combined with the opioid antagonist naloxone to prevent the drug from being abused by intravenous injection, if someone tried that the naloxone will block the buprenorphine and send the person into acute withdrawal. Buprenorphine is not a typical opioid, it is known as a mixed agonist/antagonist, meaning that the drug activates part of the opioid receptors and blocks the rest. So if someone taking buprenorphine tries to use another opioid it will have no effect, which is the main reason why it is a popular drug for treating opioid dependence and addiction. However it would have absolutely no use in treating someone addicted to amphetamines, there was no legitimate medical reason for Bonnie to be taking it.
Heroin does not widen pupils when used, the common eye changes due to heroin use is pinpoint pupils where the iris constricts.