If web activity (Clicked Link on Web Page) isn't being logged, then the sessions aren't being associated. That's kind of the definition of "not associated" (if they do accept cookies).
How are you building the link and ensuring that it is mkt_tok-enized for all users?
In addition to Sanford's explanation I seem to understand you are testing with multiple email addresses. If you are doing that from one device, you need to be very aware of which record has gone through associating the cookie last, as there will be only one cookie and depending on your link clicks and form fills the cookie is associated to only one record in your database (the last record you filled out a form or clicked on a link with).
So you need to write some good test scripts where you make sure to take the right steps in sequence to test the behaviour you want to verify. It might be wise to remove cookies altogether before you start testing with a new email address.
As you said we have made the right test cases & executed it but this time we opened the email CTA link in incognito mode for those particular leads for which the activity wasn't getting logged. Now the activity got logged into Marketo and based on their actions on the LP they received the respective email for those actions. We just want to know, we have a database in Marketo on which we have sent the emails earlier as well so for those leads also are we gonna face the same issue maybe not for every contact in our database but for some of those? if that's the case how can we resolve it?
Usually you would expect the issue to occur where you are testing with multiple email addresses on the same machine because you get conflicts with the cookies. So normally you would not get the problem with your live customer data. That being said, duplicate email addresses or multiple people having access to the recipient's emailbox can cause similar issues with the logs for multiple leads getting mixed up with eachother (because that is what happens). Another possibility, as Sanford already pointed out, is that a person did not accept cookies. In that case you are simply blind to their webpage visits.
...we have a database in Marketo on which we have sent the emails earlier as well so for those leads also are we gonna face the same issue maybe not for every contact in our database but for some of those?
Given a large enough db, there's always a non-zero chance that some of your leads will have a cookie that's already associated with a different lead from the person who received the email.
And in those cases, it's the original lead that'll get the Clicked Link on Web Page. It's not possible to avoid this 100% of the time, so it's something to document and understand rather than something to "fix."