You have a character of color, a homosexual, and/or a gender fluid character in your story, is that enough? Well, no, and I suspect you know that or you wouldn't be on this blog. Since you've taken the step to be more inclusive in your writing, you've probably tried your best to avoid anything overtly offensive but it's important to think about microaggressions in your writing, as well. This isn't easy so I highly suggest you hire a sensitivity reader (or two or three) to do a thorough check for any microaggressions and other possibly offensive things.
Let's first understand what microaggresions are in the first step to avoiding them:
Microaggressions are the everyday verbal, nonverbal, and environmental slights, snubs, or insults, whether intentional or unintentional, which communicate hostile, derogatory, or negative messages to target persons based solely upon their marginalized group membership. In many cases, these hidden messages may invalidate the group identity or experiential reality of target persons, demean them on a personal or group level, communicate they are lesser human beings, suggest they do not belong with the majority group, threaten and intimidate, or relegate them to inferior status and treatment. (Source: Psychology Today)
What do I mean when I say "well meaning microaggression?"
These are the statements that seem to be compliments but are actually negative, and as the definition above explains, targets person based solely upon their marginalized group membership.
You're pretty for a fat girl
You're gay but you're not really gay
You speak English so well
You're cool for a girl
Why is it offensive?
All of these seem like compliments but to the marginalized person they are othering and hurtful. It's like a backhanded compliment. In effect you're making that person an exception to their identity group and congratulating them for it.
What are some ways microaggressions can show up in your writing?
Microaggressions unintentionally show up primarily in character descriptions and dialogue. For example, your black character is really athletic or another character approvingly comments on your lesbian character on not being too butch.
What if you're doing it on purpose?
If one of your characters is a bigot and throws out microaggressions in regards to other characters or a group of people in general please read my other post, Tips Writing a Bigot
How to avoid well meaning microaggressions in your writing?
1. Think of your character as a real person. What would hurt their feelings, make them angry, or offend them? This isn't very easy if you aren't a member of that particular marginalized group, so hire me a sensitivity reader or consultant to help you.
2. Most of these well meaning microaggressions are directly linked to stereotypes and tropes.
Be cognizant of the stereotypes you may be relying on. Even if its seems positive (who could be angry at a "cool" black guy) but think of the voices you're diminishing when you're relying on those tropes. Be aware that these are the types of characters that have been overused to the point that we've seen them so many times your character may not even be unique.