I know for a fact there are a few “grammar snobs” here on the Chiff, so I’m asking this here 
Today, during school (the kids’ school, not mine) we were working on Adjectival Prepositional Phrases, and we came across this sentence:
The directions said to underline each adjectival prepositional phrase, and circle the noun it’s modifying, which is what I am asking you all to do for me. It is MY contention that there are two APP’s in the sentence, but the answers say only one.
Anyone?
One side of the box has a hole in it.
It’s been awhile, but I thought “side” was the noun and “of the box” was the phrase. Where do you see the other one?
Wait, are you referring to the phrase “in it.”?
Man, I just had flashbacks to grade school class chanting the list of common prepositions.
ah, Shirley…you so funny
seriously, I’ve some duct tape in the pickup
I could fix it for ya 
Yes, I am referring to the phrase “in it”. Wouldn’t “in it” be modifying “hole”, because it’s describing where the hole is (which is in the box)? And since a prepositional phrase usually follows the noun it modifies, doesn’t it make sense that this should be the APP of “hole” since it follows it? What am I not seeing here?
You’re mocking me. 
2
…entering treacherous waters…
“in it” I’d call a superfluous phrase. “One side of the box has a hole” seems to be sufficient. And the hole is not in the box, but in the side of the box, the side has the hole, the box has the side, well, several, since “one” is mentioned. Best to ignore “in it”, as it is self-referential, referring to the side, but without modifying anything (“one side of the box has a hole in itself (the side)”).
My British friend would say
“One side of the box has a hole in.”
I have no idea what to do with that…
Okay, I’m going to be a brave homeschool mom and take a stab at this.
Side (Subject Noun), has (Verb linking), hole (Predicate Noun)
“One” modifies “Side”: pronoun acting as an adjective?
Whoops, strike that, obviously a number, thus an adjective, duh.
“of the box” is an adjectival prepositional phrase, modifying “Side.”
“a” = article adjective modifying hole
“in it” answers the question, “Where.” Usually the answer to that question is an adverb, right? So I believe “in it” is adverbial and is modifying “has.” You could phrase this: “One side of the box has in it a hole.” That’s an old-fashioned construction but I think it’s still grammatical.
That said, I am running this by our grammar tutor to find the real answer. 
This is why I learned grammar by instinct as opposed to by rules.
There’s a hole in one side of the box. No point mucking around with inelegant English - just rewrite it!
Steve! I had high hopes that you would come up with the correct answer! You’ve failed my expectations 
Yay! A fellow homeschooling mother! My first instinct was your conclusion as well. BUT! If you were to say “the cookie is in the box”, “in the box” is modifying “cookie” and therefore would be an adjectival prep. phrase, wouldn’t it? “In the box” is telling more about the cookie because it’s following a linking verb. A predicate adjective follows a linking verb, and it describes the subject, not the verb. Wouldn’t that also follow here?
I also thought that it was perhaps superfluous (as hans said), but it is a prepositional phrase at least according to rules and whatnot.
just tryin’ ta be helpful… 
Hey, I could put holes in the other sides. 
Then it’d be “All sides of the box have holes.”
Then ya wouldn’t have ta worry about yer “in it” at all!
superWhat?
Thank you for solving my problem, Super Denny! You need a big “D” on your chest or something. Or a cape. I like capes. They’re almost as cool as tiaras. 
Just one of the many skills I’ve picked up here while rewording posts to something I could spell.
Shhh! Don’t disclose your secrets or else we’ll have to take your cape away!
is that better?
BUT! If you were to say “the cookie is in the box”, “in the box” is modifying “cookie” and therefore would be an adjectival prep. phrase, wouldn’t it? “In the box” is telling more about the cookie because it’s following a linking verb.
Okay, I believe (as a total grammar amateur, mind you) that in this sentence the phrase is also adverbial. My thought is that the verb “is” is intransitive. If we were to diagram it, we’d have cookie | is on the main line (with “The” stuck on “cookie” underneath) and we’d stick that prepositional phrase under the “is.” “We” might be wrong about that, though. Heh. (I’m used to the reinforcement we get in the tutorial session and the confirmations in our book.)
Anyway, I agree that the example sentence would not pass the Strunk & White test. That may be our problem.