In Sentence 1,
I'm sad to see the flowers WITHERED AWAY
... WITHERED is an adjectival complement.
If you say
"” I'm sad to see [that] the flowers HAVE withered away
...you have a different sentence structure. Here you have a main verb SEE and a noun clause direct object with the full verb HAVE WITHERED. WITHERED is a past participle, not an adjectival complement.
2. "I'm sad to see the flowers WITHERING AWAY" is grammatically correct. It describes an ongoing process without a conclusion.
3. Sentence 3, "I'm sad to see the flowers WITHER away" is about an action that reaches a conclusion but does not focus on the endpoint of the action.
When you use the bare infinitive as complement to a verb of seeing, hearing, feeling, etc. you describe the action as a whole; when you use the present participle you focus on the action in progress.
If you saw someone CROSS the road, s/he reached the other side; if you saw the person CROSSING the road, there's no indication that s/he reached the other side.
That's why you would be more likely to say
I saw you EATING a watermelon at the company picnic
"” ?I saw you EAT a watermelon at the company picnic