Why Are the 3, 6 and 9 not Properly Aligned, at the Baseline, with the other numbers in my Chapter Heads?
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That’s the way that they were designed, by whomever it was that created the Caecilia font. (There are a few others that work this way, too.) The number alignments for those digits fall below the normal baseline. See below for an example. This occurs in other fonts and typefaces, as well, but it’s quite prominent in Caecilia.
As you see with the font Caecilia in this case, it is not uncommon for some numerals, like 3, 6 and 9, to drop below the font's typical/normal baseline. This is stylistic, and not an error.
This is normal, and not a mistake.