I've noticed it too. I really enjoy the series, but I don't even bother with fanfic. I think there are several things that lead to Percy Jackson fics being even more riddled with Sues than average.

One, the series is very welcoming for OCs. Demigods canonically are reasonably common and can turn up anywhere, anytime. They also tend to turn up when they're 12-16 - perfect Standard Sue range.

Two, these kids that can turn up from anywhere are already by default half-human half-(something super awesome). This is already a common Sue trait - and this is canon. It's also very easy to give these characters superpowers and/or tragic pasts.

Three, the series is geared towards exactly the age range that writes Mary-Sues the most.

And, most importantly I think, four: There is a hot single guy. Never underestimate the power this holds. Nearly all the PJO Sues I've found go after Nico di Angelo. He's a hero with a dark past and Kool Goffik Death Powerz. Think of all the Legomancers in LotR fanfic - Nico is PJO's Legolas, in this respect.

(Just putting this out there: I love Nico. I think, after Annabeth, he's my favorite character from the series. Unfortunately, the Suethors seem to share this opinion.)

As July said: if you think a character you're writing is OP, it probably is. Other words: It's really, really, really easy to screw up when writing a demigod and end up with a 'Sue/'Stu in your hands. But, as noted elsewhere, OPness does not necessarily mean Sue. Sues have more traits than just OPness.

That's what those teenagers are. So it is not unusual that you think that they are Mary/ Marty Sues. But I only watched the movies.