It really depends on your ability to identify parts of speech regardless of the 'ing' ending. If you can spot adjectives, nouns and verbs, then you will be able to work out which function the 'ing' word is playing.
He is coming.
'Coming' is not the 'main' verb here, or not alone. Rather, 'is coming' together is how English forms the present continuous tense (i.e. verb 'to be' + present participle).
The report that the island is under the water is misleading.
In this sentence, you need to work out what function 'misleading' is playing. Is 'is misleading' a present continuous action being done to something?
John is misleading people/things. [Present continuous verb being done to the object of the sentence.]
Or is 'is misleading' describing the subject?
John is misleading. [John is a misleading person: misleading is used as adjective.]
John's misleading is wrong. [Misleading is used as a noun. @Fumblefingers' rule works here to show it is a gerund ("the action of misleading").]
You could reword you sentence as:
The misleading report that the island is under water.
So here, misleading is acting as an adjective describing the report.
So I suppose my overall advice on how to work out the function that an 'ing' word is playing would be to try to reword the sentence in a way that makes the function obvious.