Can you tell a bit more; does the 3HR work normally with other activities (running, cardio, walking)? Has pool swimming worked correctly in the past? Is the recorded time duration of the swim correct? Is any distance recorded, or is distance 0? Are you sure you did not mistakenly enter a pause or drill?
You could try to reset the Pool Swim activity to defaults. Hold UP, select Settings, select Apps, select Swim (Pool), and then it is the last option Reset activity to defaults (as far as I remember, I am writing this without having the Fenix 3 here).
If that does not work, it's best to reset the device according to the instructions in the manual, here: fenix_3_HR_OM_EN-US.pdf
