Better times to use the "I have a bad feeling about this" line
Episode I: In the final battle after Qui Gon and Obi Wan clear out the hangar, Qui Gon stops for a second and says "I have a bad feeling about this" and then a little while later the door opens and there is Darth Maul
Episode II: As Anakin and Padme are arriving on Genosis and they are walking through that tunnel and Anakin can hear all of the little aliens behind him
Episode III: Instead of Obi Wan saying "It's making me feel uneasy" he says "I have a bad feeling about this"
The line is supposed to be used in situations where the characters sense there is danger ahead of them but they're not quite sure what it is.