If you're seeing red pins with a warning triangle over shops and enclosures, these are not connected to the entrance via a path.
Make sure you not only have paths next to all of your shops and enclosures, but also that these paths are connected to the zoo's main entrance. It's a good idea to rotate the zoo and follow the paths with your fingers to make sure there aren't any gaps anywhere.
You can purchase paths in shop under Buildings > Paths. Paths can be placed and moved just like any other decoration.