The short answer is no.
Regarding the composition of replicated food, the TNG Technical Manual (considered to be a fully canon reference guide) specifically states that food replicators are capable of producing food molecules at sufficiently high fidelity to provide all needed sustenance with no adverse effects:
"As with all transporter-based replication systems, the food
replicators operate at molecular resolution. Because of this, there
are significant numbers of single-bit errors in the resulting
replicated materials. These errors are not nutritionally significant
(although some individuals do claim to be able to taste differences in
certain dishes), but certain types of Altarian spices have shown a
tendency to become mildly toxic when replicated, so their use is
avoided in replicated dishes."
Miles O'Brien (a transporter and replicator specialist) casts scorn on his mother's prejudice that replicated food doesn't provide the same high quality nutrition:
KEIKO: She cooked?
O'BRIEN: She didn't believe in a replicator. She thought real food was more nutritious.
KEIKO: She handled real meat? She touched it and cut it?
O'BRIEN: Yeah, like a master chef. She was fantastic. Of course, I'll have to use the replicator, but I'll make something special for
you tonight. You'll love it, I promise. - TNG : The Wounded
If anything (as we see in @Tritium21's answer) it's actually the opposite. The replicator allows you to artificially control the levels of fat, sugar and protein in your food and will actively resist you trying to make something damaging to your health:
TROI : And computer, I'd like a real chocolate sundae.
COMPUTER : Define "real" in context, please.
TROI : Real... not one of your perfectly synthesized, ingeniously
enhanced imitations... real chocolate ice cream, real whipped
COMPUTER : This unit is programmed to provide sources of
nutritional value. Your request does not fall within current
guidelines. - TNG : The Price
It's not uncommon for characters to disparage the taste of replicated food, but there's no indication in either the TV show or the other canon materials (writer's guides, technical manuals, etc) to suggest that replicated matter is actually bad for you.
WILDMAN: I thought you didn't use replicated vegetables when you're cooking. Always fresh, organic, from the airponic bay.
NEELIX: Well, the yields have been a little low lately. Normally, I would never dream of using synthesised veggies. - Voy : Deadlock
EDDINGTON: Replicator entree number one oh three. Curried chicken and rice with a side order of carrots. Or at least that's what they
want us to believe. But you and I both know what we're really eating.
Replicated protein molecules and textured carbohydrates.
SISKO: It's not that bad.
EDDINGTON: It may look like chicken, but it still tastes like replicated protein molecules to me.
SISKO: If you don't want it, don't eat it. - DS9: Blaze of Glory
JOSEPH [on monitor]: Whatever you do during the day is your business. But at dinner time, you better get yourself down to New
Orleans. No son of mine is going to eat that replicated slop Starfleet
calls food. Not if I have anything to say about it. - DS9: Homefront
SEYETIK:...Which reminds me, wait till you taste the food my wife has created for you. None of that replicated nonsense you're used to.
No, every dish was prepared entirely by Nidell's own sweet hands. - Second Sight
SISKO: Maybe you need a vacation.
LEYTON: Mmm. Somehow replicated coffee never tastes this good. I'm afraid I owe you an apology, Ben. - Paradise Lost