What you have here is ghosting, rather than lens flare. Ghosting produces a secondary image of the bightest object(s) in the shot. Flare produces either an overall reduction in contrast or an aperture-shaped spot reduction in contrast (or both).
Ghosting is caused when light passes through the lens, is reflected off the sensor back into the lens, and reflects off one or more elements and back to the sensor again. While it happened with film cameras, it is much more common with digital cameras because the sensors are much more reflective than the emulsion side of film.
Filters are notorious for causing ghosting because they are flat. Flat surfaces reflect better.
Digital-grade lenses (all Canon and EF lenses manufactured in September 2000 or later and all EF-S lenses , Sigma DG and DC lenses, Tamron Di and Di-II lenses, and Tokina D and DX lenses) have special coatings to reduce ghosting. No lenses completely eliminate ghosting.
Ghosting always occurs, but is virtually invisible when the ratio between the brightest areas and the background is low, as with most daytime shots. When you have a high contrast ratio, however, the ghost appears.
Techniques to prevent/minimize ghosting include:
-- A careful choice of lenses (some are much worse at ghosting than others).
-- A careful choice of angles so the ghost misses the sensor, or is cast where the background is brightest.
-- Removal of all filters. If a filter must be used, be sure it has anti-refelctive coatings, which help prevent ghosting—somewhat. There are special anti-ghosting filters with curved surfaces, but the are very expensive and rarer than hens' teeth.
-- Use a polarizer. Yeah, I know a polarizer is a filter, but in some cases it can help with ghosting. This is especially true when the bright source causing the ghost is itself a reflection, i.e., polarized light.
-- Use as low an ISO as you can. This can often place the ghost in or near the "mud" at the bottom of the sensor's sensitivity range, rendering it invisible (or very neary so).
-- Shoot wide and crop narrow. By shooting with a wider angle of view than needed, you get a lot of extraneous material around you subject. Often, the ghost can be manipulated to be in this extraneous material. Then, when you crop the image to your subject, voila! No ghost!