Waypoints are a tool that sends your boat to specific coordinates automatically in your absence.
When you don't touch them, they are very accurate. Your boat will make it to the first waypoint coordinates, then change its course and head straight to the next waypoint. Waypoints are the best way to sail close to the coast, but in order for them to work efficiently, you have to trust them.
When you watch your boat move on the map, the movement you see is based on the latest data exchanged between your computer/smartphone and the game server.
This means that what you see on your screen can be slightly out of date compared to what is really happening on the server. If you change the position of a waypoint, this can lead to backdated course changes that will only be taken into account during the next run of the engine's calculation, which can generate annoying situations such as a grounding, or a buoy not being validated.
That's why it is important that you plan your navigation carefully. Place your waypoints away from the coast, then let them do their job, and try not to interfere: your boat will eventually reach its destination by itself.