Input file

I don't believe you can have elements listed in the CONNE block if they aren't in the ELEME block. Have you tried running a simulation with the input file? Also, could you provide a few more details about these elements? Better yet, could you attach the input file?  

It's obviously impossible for me to tell you exactly what's going on, given the size of the file, but here are a few observations:

1. Element A1166 is indeed missing from ELEME block, although it's shown as being connected to A1165 (located just under it). 
2. In addition to A1166, there are also a number of other elements present in the INCON block (numbered A1166 to A1199 and F11 1 to F1121) that all have similar definitions (100% porosity, about 1 bar of pressure, nearly dry gas (depends on EOS), and 20 degrees C) that are missing from both the ELEME and INCON blocks.
3. Elements A11 1 to A1165, which do exist in the ELEME block, all have the same conditions defined in INCON as those described in item 2 above.
4. According to ELEME block, A11 1 to A1165 are all assigned to the SURWA material name in the ROCKS block (presumably for surface water source?).
5. According to the first line of the CONNE block, A11 1 to A1165 are all connected beneath element A1  0, which is the only element assigned to the ATMOS material name.

It's hard to conclude much, but I think these missing elements were meant to be included with the other SURWA types, perhaps as another layer?  Somewhere along the way, they may have been partially removed from the input file.   If I were you, I'd start with removing the listing including A1166 in the CONNE block and removing all of the INCON items listed in #2.  Be sure to make a copy of the original, of course.

By the way, which EOS are you using?  Based on what I can tell from your input file, I'm guessing 3 or 9?

According to Table 9 of the TOUGH2 User's Manual, the second primary variable is a listing of air mass fraction for single phase or of gas saturation + 10 for two phase.  So what 0.003 indicates is a single-phase liquid, which is a mixture made up almost entirely of water with 0.3% mass fraction of air that dissolved into it.  In two-phase scenarios, you'll see a number listed between 10 and 11, which is the gas saturation + 10. 

Also, back to your original question about missing elements: I noticed when starting to run your case that the missing elements were ignored by the code.  I suspect what may have happened is someone ran a simulation to steady-state to establish initial conditions for a subsequent run, where the boundary conditions where altered by removing the missing elements, which would impose a no-flow boundary where they used to exist.

Madjid,

1 - I'm almost certain you cannot assume it's reached steady state.  If you assign a time to reach, even if your simulation reaches "steady state" by the definition given in the TOUGH2 source code (i.e., when the simulation would otherwise end if a final time weren't assigned), it will continue running until your desired time is reached.  In order to know for sure, though, you should read your output file to see the reason your simulation ended prematurely.  This information should be written in the output file right before the data at the final time step is reported.

2 - I don't know the answer to this question yet.  Give me some time to investigate it and get back to you.  Unless someone else who does know would like to chime in. : )