No, there was never any line down Carlton St. and, so far as I know or can find out, no temporary or service track. even when they were building the Governor Square extension. all the temporary stuff was east of St. Marys St. I wonder what you saw? The only lines connecting/ crossing Beacon St. from the south, west of St. Marys st.) were the Longwood horsecar line, at Harvard St. later the Allston Line crossed there and, a line came up Washington St. from Brookline village. Reservoir was always the only barn on the line. The Beacon St. line was built right at the beginning of the electric era so, historically, it is well documented. Before that, the only transit in that part of town was the aforementioned horsecar line up Longwood from Huntington Ave. in Roxbury.
LS