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The combination of amitriptyline + methadone carries a risk of sudden cardiac death. This is because both drugs affect the heart and its electrical conduction system.

Methadone is the only opiate for pain that does this:

This older post of mine explains it in detail:
http://neurotalk.psychcentral.com/post15298-4.html

This special website goes into more detail:
http://www.azcert.org/

Even people only using methadone can be at risk. When you add other drugs which also do the same thing, you get a much higher risk. Add to that a case of stomach flu...with a loss of potassium and magnesium and you have a triple risk.
Add to that a genetic flaw in heart conduction and you have a far greater risk again!

Amitriptyline is an antidepressant in higher doses. At the 10-25mg a day dose it is less so. As you increase daily dosing it starts to work as an antidepressant.

All people using methadone should be screened by the doctor for prolonged QT risk. And then if methadone is increased, periodic EKGs should be done. The patient should also guard against losing electrolytes while on therapy because this can tip one into a conduction emergency if they get low.

As far as amitriptyline making people depressed? All antidepressants carry that potential. Mostly in the beginning of use they are sedating. The SSRIs have a history of increasing serotonin in some people genetically prone to suicidal thoughts. This is less likely with TCAs like amitriptyline. But mixed with an antiseizure drug like gabapentin, or Lyrica or other similar drug and then TCAs may tip into suicidal ideation--since the antiseizure drugs cause this too.
This does not happen in everyone however.

Your biggest problem with this combination is the cardiac risk.

I really cannot imagine a pharmacist telling you there was no problem. This combination is well known and should be on the pharmacy's database and should FLAG this interaction and stop the pharmacist from filling the two drugs together.
example from drugs.com :
http://www.drugs.com/interactions-ch...t=168-0,1578-0

Please read the link above carefully.