Once you know the twist ending a lot of things make sense - like why if you watch closely, Cole is the only person who ever pays attention to Malcolm even when other people are around.
Also, Malcolm wears the same blue shirt throughout the whole movie.
Not true! You see him wearing a grey sweatshirt at many certain points. He also goes back and forth between wearing different coats and jacket
If you watch the opening scene closely, everything he wears during the rest of the film is something he had on at one point or another during the opening.
You also never see the back of the shirt, which is covered with blood from the exit wound.
When Vincent shoots Crowe and then himself, on the surface it seems like an unstable man in the heat of the moment. However after it turns out Vincent also sees dead people, it would seem he offed himself so he wouldn't have to endure Crowe's spirit haunting him.
Notice the incident where Cole loots a religious figurine from a nick-knack table in the first church scene. Cole is likely reacting to his latest ghostly "friend". Notice that the figurine has the color red too.
Cole is naturally terrified of the ghosts because of the way they look (often grotesque) and their violent actions. Scary enough for a kid his age, but there's a scene where his mother looks at a baby picture - seeing an unusually scared baby and a wisp of light in the background.