How to describe situation when two people can't meet?

If two people cannot schedule something at a mutually agreeable time, one could say that they cannot coordinate or cannot coordinate schedules. This represents a deliberate attempt to meet, so it wouldn't apply particularly well to two friends who never happen to meet by chance at a shop they both frequent, however. The term is a bit formal, more commonly used in a business setting when scheduling meetings - pehraps a more informal option would be to say that two people's schedules don't line up.

When this happens by chance over the phone, it is called phone tag. One person calls the other, but they don't pick up. That person then either sees the missed call or hears a message on their voicemail, and calls the first person back. The first person doesn't pick up, and must call the second person back, and so on, and so on. This is aptly described as a game of tag, with the person who missed the call being "It", and having the responsibility to attempt to re-initiate contact.

[did not] coincide

Definition of coincide

intransitive verb 1a : to occupy the same place in space or time The base of the triangle coincides with one side of the square.

would be a word that conveyed that they never were in the same place at the same time but does not imply anything about coordination or lack of it.

One option is the verb connect

Defined in The Free Dictionary:

connect (with someone) in. to meet someone; to talk to someone on the telephone. For your We connected over a drink and discussed the matter fully.

Another is the verb run into

1. Meet or find by chance, as in I ran into an old friend at the concert. [c. 1900]

connect has an aspect of planning to it while run into has an aspect of happenstance.

Your examples might become:

Example: John and Michael are friends. They both shop at the same place every day, but they have never met. John is saying: How come we shop at the same shop, but we never seem to run into each other there.

I think above example wasn't the best one cause it suggests a coincidence. Let's try another.

John and Michael are friends... obviously. They want to stay in touch, but every time one calls another, one of them is busy or not available. They cannot find a proper time to talk.

In this case the attempt at planning is seen and an option might be:

John and Michael never seem to be able to connect.

One more example.

John and Michael are... working in the same company. They need to discuss something really important so they want to have a meeting. John called Michael to arrange one, but Micheal was in another meeting. A few hours later Michael run into John and asked about the meeting but John was about to leave the workplace. They just cant find the time when they're both free.

Here again connect seems appropriate:

John and Michael just can't find a good time to connect.