Happened twice in the same season -
7th Sept 2002 - Morton 2-3 St. Mirren (Hoppy scored our 2nd) and Faroes 2-2 Scotland (this kicked off when our 2nd half started) Not a good day.
29th March 2003 - Gretna 0-1 Morton (Eddie Annand) and Scotland 2-1 Iceland (Kenny Miller got one).
Morton played Alloa on 12/11/05 at the same time Scotland played the USA at Hampden. I went to the Scotland game whilst the rest of our regular group at the time went to the Alloa game.
Three times that season. Morton beat East Stirling 1-0 at Firs Park the same night Scotland lost 2-0 to the Republic of Ireland at Hampden in a friendly.
I'm sure there has been a more recent club v country clash that coincided with a Scotland away tie.