the website/app doesn't know for all trains the information if you need a reservation or not. 

It depends from country to country, but most of it local trains like Regional or Regional Express are reservation free. Long distance have optional reservation like Germany, Austria or Switzerland and in some others you need a reserbation. You can check on the interrail.eu website/app information about a country and also in the planner of tje train companies (when it stands reservation compulsory or Global Price = reservation needed). 

If you have further questions about some trains ask here. We can help.

The planner/app is based on a normal plannner of a railway-and has added features like need to RES or not-etc. There are however in SOME countries also SOME railways that do NOT accept passes-you have to pay normal ticket. This f.e. also even in PT: the Ferrotagus over the bridge near Lisboa.

For some specific trips it is needed to use those short links however-but without you giving any ex. it is hard to say what/which