I'm attempting to make lots of custom break on a coffee mug (currently I only have one and it isn't working properly). When I hook a grid part of the grid becomes part of the shatter and the handle not only separates from the cup but the handle shatters even though the grid doesn't cross it.

for your case select Break SOP and in Boolean Settings uncheck Check for Full Enclosure checkbox
additionaly it may help with further cuts if you prepend polycap as your handle is not closed