I work with digital topo maps that often have clues about forgotten branch lines. While I have never been to Machias in my life, I did find a couple of interesting things on the maps.
(Note: I have traced over the rail lines - or trails - with a red dotted line so to highlight the route.)
Map 1: Downtown Machais:

There was a branch that left the main line, curved southwest, crossed route 1 and ran parallel with it. The topo indicates a siding where I have noted on the map. There was also a shorter branch to the north. A historical topo from 1918 shows multiple tracks crossing Route 1 to a small yard/industry. Unfortunately, current aerial photo seems to reveal a good deal of construction in the area that may have obliterated these branches. Regardless, it might be worth a look.
Map 2: Whitneyville Industrial Track:

West of Machais is Whitneyville which was also served by a spur. Again, it's probably gone, but worth a look.
Where it gets interesting is maps 3 and 4. Neither actually show an official railroad grade. However, given their shape and the surrounding topographic features for fills and cuts, they very well could be. (They also could be trolley lines, which are often omitted from topo maps.) I checked our historic map collection and there is no indication on either of these lines that they were or were not railroad related. The first is my best guess to a branch from a point near Machais towards Machaisport.
Map 3: Machaisport Branch?

Unfortunately, as annotated on the map, this trail does not actually connect to Machaisport. Instead, it starts and stops, seemingly, in the middle of nowhere. Does anyone know if a railroad (or trolley line) ever used this alignment just south of Machias?
Map 4: Jonesboro Branch?

Finally, this line has the look of a spur, especially how it curves away from the Calias branch. However, it also turns into a dirt road (which is shown on the historic topo maps.)
I don't know if any of these help any would be rail-hunters.