If the answer doesn't affect meaning, let it go while they're reading the first time, and if you have time and it's a word or expression they need to know, you can ask them to take a closer look at the whole sentence the second time through. If the answer affects their understanding of the passage, give them a chance to correct it themselves, but if they get to the end of the sentence and still haven't corrected it, then ask them to take a closer look at the sentence. You want them to problem-solve words in context, so don't point out individual words, and always phrase it as, "You need to take a closer look," not, "You made a mistake, fix it." And if they get embarrassed, tell them that good readers say the wrong words all the time, but if it doesn't affect the meaning, it doesn't really matter. So in some ways, those kinds of mistakes are good - it shows that they're understanding more of what they read.

That said, the reading tests do not make any difference between miscues that don't affect meaning and those that do (which IMO is pretty silly, but anyway.) The tests expect 97% accuracy, which allows for about six mistakes per page of text in a novel. If they're making fewer miscues than that, meaningful or not, don't sweat it; if they're making more, get them to reread.