Hi Stefan,
The most likely reason for this is that the LTE isolines are based on a transport calculation, i.e., they include the effects of diffusion and dispersion. If the layers are relatively thin, the default transverse dispersivity will lead to a similar distribution of LTE in the different layers. You can test this by applying the random-walk method as well (=pathlines with dispersion). I'd expect that the result will be somewhat similar to the LTE isolines. Another reason could be that the aquitards consist in only one layer. LTE concentration then can also be passed through the aquitard more easily than realistic.
To know what the 'real' distribution is, you'll have to apply realistic values for dispersivity plus a subdivision of the aquitard(s). Note that using small values for dispersivity may require a fine discritization, especially in vertical direction, in order to obtain a stable transport solution. This is similar to a mass or heat transport simulation.
Cheers,
Peter