The only consequence is that most filter frames that stick out will allow air to be sucked into the return air plenum which can create a negative air pressure area close to the furnace burners of the furnace.
This can be a problem for natural draft or 80% furnaces with borderline venting. Some folks deal with this by using a wide strip of cheap painters tape to bridge the filter gap where the air is being sucked in. Just make sure that there is no way that the tape can be sucked into the furnace or it will cost you $$$.
For one, stop using the 3m Filtrete filters, they are not needed. If someone has allergies, you really should be using something like the Aprilaire system, not a replacable over priced filter. All we use in my furnace, is a washable filter, that gets cleaned once a month, and does a better job than those 3m filters.