It's not a flaw in the game, it's how it was designed. Rested xp is a percentage of your xp bar, not a static amount. At level 1 your bar fills up a lot faster than at level 49. Using your rested xp on a level 1 job as you did, is a waste.
And where, exactly, were you waiting out time between your storyline dungeons and stuff, and where did you log off? Was there a big glowing crystaly thingy? Yeah, dude, that's a sanctuary. All towns with an Aetheryte, and your inn room in cities are sanctuaries where you earn rested xp even while logged out of the game. You do not earn rested xp by doing ANYTHING but standing in a sanctuary. You can tell that it's a sanctuary because of the little crecent moon icon near your xp bar, FYI. Next time you build up rested xp, don't waste it on a level 1 job. Now you know how it works. You got a tutorial entry on this the first time you stepped into a town with an aetheryte. You can go look it up in your logs ingame right now. Allowing static amounts would break the game, making it far too easy to level alternated classes up. Not that it's all that hard anyway. It's called balance.