Several things I have noticed with my current game and mapping issues:
1. Workers make a decision about where the highest priority is, so if they are on automated they may decide to run off to the far reaches of your map.
If they bump into an obstacle on the way that wasn't in their path when they started - such as another countries unit - they stop dead, they don't know what to do.
In one instance I manually took over the unit in question, backed him up to another location, hit CTRL-A and he ran straight to the same blocked point.
2. I had Right of Passage with several allies as we pounded upon the Greeks. The problem came with several geographic bottle necks in the terrain .. my allies would park units there and we were unable to get passed. Automated units would grind to a halt, military units moving from A to C would grind to a halt.
With a Right of Passage, I think there should be an option to attack or move through, or something.
3. Several workers walked between two squares .. one rail, one road, back and forth several times ... without actually doing anything.
4. I had a cannon path a route through a mountain ... which, ofcourse, it couldn't get passed. Not sure wat this was about. It's almost as if the rail going through it was the only thing the cannon could see.
5. In the same vein, a sprawling rail and road network had one square blocked by an allied unit. They happened to be on a section that was rail and had road either side.
My automated unit was so desperate not to leave the rail road, that he couldn't figure out how to step off, go on the road, and go around. Again, staying on rail seems to have such a priority that terrain, other units and alternative routes don't seem to come into it.