What do pink-highlighted squares mean?

No, this same pink background is used for two different "errors".

First one, and the one most people are familiar with, is the Missing Fonts marker. That's what happens when you open or import a document that was formatted on another computer, with differently named fonts, or when you applied formatting to a font in a style that's not available (fer instance, you tricked ID in applying Italics to the font Gisha).

Missing Fonts can be easily found & fixed, since they are listed in the Find Font dialog.

The other error is more insidious: the character that some font is applied to, has no representation in that font. So InDesign does two things: first, it shows the pink background; and second, it shows the "missing character" image of that font (which usually is some sort of crossed-out square ... but not always).

Since the "underlying code" of the character is still there, all you have to do is apply another font to just this character.

The error is properly called "Missing glyphs", because a 'glyph' is what a certain character representation is called in a font.

So, it's either a missing font or a missing character? Alas, no.

InDesign's import filter for Word contains lots of errors. Lots. And I mean it. This causes all kinds of weird things to pop up in imported documents, and it sometimes manifests itself as really really weird "character codes" which should really not be appearing at all in any document! (Which is, incidentally, why they appear as Pink Missing Glyphs -- they would not be found in any sane font).

A couple of them I have come across:

<?> -- yes that's how it appears, it's a Footnote Number Code gone Bad. ID imported a footnote but doesn't iknow what number it was.

0xE000, 0xE001, 0xE002 (and so on) -- internal InDesign 'placeholder' markers. They are present inside the InDesign document itself, but they should not ever be visible to the user.

0xFFFD -- the official Unicode Replacement Character. Inserted by InDesign when it really should have something inserted something else (a footnote, or a table, or an inline image, or (at times) something quite unclear when there wasn't anything in the original Word document).

0xFFFE -- the official Unicode Not A Valid Character character. This code is officially documented as "Not Valid", and ought *never* appear in any valid document. ID still inserts it. 'Nuff said.