All the possible explanations considered so far "defy our current understanding of Mars’ upper atmosphere", according to the researchers.

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Strange show spotted high above Mars’ surface remains mysterious
Amateur astronomers saw it, professional astronomers aren’t sure what it was.
by Scott K. Johnson - Feb 16, 2015

Almost three years ago, the Red Planet put on a bit of a show for anyone with a telescope big enough, and an eye trained enough, to spot it. As the Terra Cimmeria region of Mars’ Southern Hemisphere rotated into view, a faint bulge rose above the smooth curve of the planet’s surface. It looked like a cloud, but it was too tall and too weird.

Starting on March 12, 2012, amateur astronomers reported seeing the odd lump on the Martian horizon. Reports continued to pour in over the next 11 days as the lump became even more obvious. It petered out some time before April 1, but a second occurrence was observed between April 6 and April 16. Each time, its form varied from day to day, and it was seen as dawn swept across the region—but not at dusk.

Although the Mars Reconnaissance Orbiter imaged the area daily, it did so in the afternoon, and nothing showed up. But using the images that were captured by amateurs, a group of researchers led by University of the Basque Country’s Agustín Sánchez-Lavega calculated the size of the fuzzy plume. It covered an area some 500 to 1,000 kilometers across and reached as high as 200 to 250 kilometers above the surface—that is, into Mars’ ionosphere and exosphere.

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http://arstechnica.com/science/2015/02/strange-show-spotted-high-above-mars-surface-remains-mysterious/

Link to PDF of scientific article in the journal Nature

If the above Nature PDF link doesn't work or goes to an abstract, try the link labeled "DOI:" at the end of the arstechnica article.