Can I run factor analysis on items that are measured on two different 5 likert scale, that is one scale is measuring frequency ( i.e never , rarely, occasionally, frequently and always) and other agreement ( strongly disagree, disagree, not sure, agree and strongly agree)
Well, you could do this but why would you?
Factor analysis starts with the correlation or covariance matrix of the items you include. Then it tries to find patterns in order to create latent variables.
What will you do if you find a latent variable that includes both frequencies and agreements? Will that be of any interest? Will you be able to use that latent variable to do anything?
Probably the answers here are 1) Be confused 2) and 3) No.
If that's the case, there is no reason to do the FA this way.