Unfortunately, it is possible to miss some Djinn in the game very easily. While many Djinn appear in plain sight (though usually out of easy reach) in towns and dungeons, others are hidden away off the main path. For example, the most recent Djinn I collected was hidden in a remote corner of a large, hard to explore desert dungeon, and could only be seen by using the Reveal spell. Even though that desert requires the player to constantly use Reveal, there is still a good chance a player might miss that Djinn if he doesn't put in the effort to search over every inch of the desert.
While it is not that hard to get every Djinn in the towns and dungeons, the real offenders are the Djinn hidden on the overworld. These Djinn only appear if the player fights a random battle in a specific, very limited section of the overworld. There are no visible signs that a Djinn is hiding in these locations, which are usually far away from the main roads connecting the towns and dungeons. Furthermore, if there are clues in NPC conversations as to the locations of these Djinn, I haven't seen them. The only reason I know where these Djinn are is because I checked GameFAQs. The difference in difficulty in finding these Djinn as opposed to the rest is monumental.
Unfortunately, there is no way for the player to be certain that he has even missed a Djinn. There is no set order in which the Djinn become available. While one set of four appears in the order of Jupiter, Venus, Mercury, Mars, the next set is Mercury, Jupiter, Venus, Mars. Even more problematic is that the sixth Venus Djinn becomes available before the fifth Mercury Djinn. The player might falsely assume he missed one.
While I don't think the hunt Djinn should be made too easy (since it is a fun collection quest), there are ways to eliminate the really frustrating elements. First off, the game developers should leave clues as to the whereabouts of most of Djinn. While this could take the form of information given by townspeople, it could also include some kind of Djinn radar that tells the general locations (the name of a town/dungeon/overworld region) the Djinn are located in. Also, fixing the order in which Djinn appear into a specific pattern could leave clues to whether or not the player has missed a Djinn, from which he could surmise where the Djinn could be. Finally, the problem of finding Djinn on the overworld could be fixed by creating a visible marker of a Djinn's presence, such as the circling form that Flint took at the beginning of the game. Any one of these solutions may be sufficient.