I am looking at A 2016 Ford Focus se with 38,000 mile on it. It has the 5 speed manual transmission and 2 years left on the factory Warranty. Is there anything I should look out for ? are they any common problems with this car ?
https://www.carcomplaints.com/Ford/Focus/2016/
Just note the transmission issues are not relevant to you as you have a manual. They are cheaper made cars but should last you a while as the transmission is a manual.
is the rest of the car pretty well built ?
No they are economy cars most of the cars in the segment are cheaply made even the Corolla was not very well put together compared to the Camry and Avalon. It could last engine and transmission wise though.
That is pretty low miles it could still last a while especially if you are getting it for a good price I see those go for 4 5 6 grand all day long with very low miles,
Worst case scenario sell it after the 2 year warranty.