OK i found the/a solution.
It looks like a bug in the Meshlab GUI. I have tested the same filter script with meshlabserver on several hundreds models and the error never appeared. In the GUI it only comes up if you use the poisson filter twice ore more (even on different projects). If i restart the MeshLab GUI for each file the error never appears… this looks like some kind of global variable not being reset with a new project.
Since MeshLabServer runs once for each file this bug doesn’t bother me there 
Originally shared by Christian Lölkes
Hi, i need some help with meshlab. I made some scans with the kinect and want to apply a poisson filter (11/7/1/1). Sometimes it works really great but with other models i get this strange stuff.
While browsing the internet it looks like nobody else has these problems.
Things i do before i apply the poisson filter: remove non manifold edges and vertices, close holes, reorient all faces coherently, normalize faces normals and vertex normals, quadric edge collapse decimation (500k), close holes, remove non manifold edges.
I tried a lot in different directions but it looks like i miss something and it is getting really frustrating… Maybe you can help me.
I use MeshLab v1.3.2_64bit on Windows 7.
