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If I say "I tend to agree on what you said" Does that mean I totally agree on what you just said?
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No, not totally; just somewhat.
I do not fully agree with what you said but I do agree with most elements or the overall principal of your position on the issue.
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Jonathan MarianuI do not fully agree with what you said but I do agree with most elements or the overall principal of your position on the issue.
If the speaker feels comfortable with the other the next statement is typically "However .............." which is a clarification of which of the arguments they disagree with.

"Tend to agree" can also be used if the speaker is not comfortable speaking freely to the other yet wishes to politely say "I do not fully agree with you." The word "tend" is said more slowly and the intonation is different in that the inflection drops after "agree" so as to indicate there will not be a further statement and that the speaker wishes to discuss a different topic.
samerrustomIf I say "I tend to agree on what you said"
This is odd. People normally say agree with, not "agree on".
Jack and Jill agree on the issue.
Jack agrees with Jill.
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Jonathan MarianuJack and Jill agree on the issue.Jack agrees with Jill.
They could also agree with what Joe Bloggs said.

Stating that one tends to agree communicates that, at this particular moment in time, one agrees with your statement. It is merely taking into consideration that opinions may change.