A simulation will not stop when a constraint is violated, but a message will be printed.
Not all validation rules in the spec are checked.
Error messages have inconsistent format (older ones have orange and lots of bright red that needs to be changed to be consistent with the black/blue format).
Off-line users guide has not been revised since 2.4
SBOTerms are tracked in the verbose listing but nothing else is done with them. There are currently no hooks into the SBO database, although such options are planned in the future.
MIRIAM support is limited to writing a creator block to the head of the file. Normally this is done automatically by createModel but the user can supply some of the information through options. The default user information (Family, Given, EMAIL, ORG) is only as accurate as the user information provided by your operating system.
The csymbol "delay" is not implemented in SBMLNDSolve, and attempting to run models with delays will lead to errors.
MathSBML will sometimes ignore extraneous XML objects that are embedded in the SBML without giving an error message.
Varible names in models may cause conflicts with system variables when using context->None in SBMLRead. Examples are E (exponential), F (Elliptic function), and Pi (the number pi).
MathML translations are performed using the built-in Mathematica translator: this means that some things will appear odd, e.g. A/B becomes A*B^(-1), etc.
Mathematica may internally rearrange formulas, so if a model is input and then output, the formulas may "appear" different (but are still mathematically equivalent).
Simulations may not be run with models that contain only assignment rules, or only algebraic rules, but have no reactions.
Interpolating into solutions of SBMLNDSolve at t=0 may result in a value that is slightly different than the intial conditions because of mathematical roundoff and numerical interpolation error.