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Even with the most scrupulously set H&J values, type composition programs will sometimes set type badly. These missteps fall into two general categories: those that affect lines or groups of lines and those that affect page layouts. Some programs offer mechanisms to avoid or lessen the severity of layout problems, but problems in lines of type usually require you to go in and tinker by hand.
The most common composition problems are lines that for one reason or another can’t be set without violating the limits you’ve set for how much word and letter spaces can be altered. Programs are generally written in such a way that when these situations arise, lines will be set too loose rather than too tight.