Post the inconsistencies and plot holes you've found here. :P
Well so far I've found only 2 of them.
1. Chapter 75, 189, 190 - this is about Chachamaru. I just find it really odd how she's not flustered or embarassed when facing Negi naked in chapter 189 but on previous accounts(chapter 75) and the latest chapter you can see that she's extremely shy with Negi.
2. Chapter 162 - Maki and Ayaka's intrusion on Chao's farewell is ummm... well it's wrong. They're not supposed to know about magic and on later chapters they're still ignorant about magic despite seeing Chao floating in mid-air and initiating a time travel.