I have gone through several websites and what I have concluded regarding the difference between marked with and marked by is that the former refers to actual markings, while the latter can signify some abstract concept. Yet this difference seems superficial when I think about it for long.

Which looks more appropriate of the two?

  1. The politician's speech was marked with scorn for the rival party.
  2. The politician's speech was marked by scorn for the rival party.

Solution 1:

I think there is a little more to it than the passive.

(i) It was marked by a hard, sharp object - "by" introduces the agent and the agent does the action of the verb.

(ii) It was marked with a red X - "with" introduces an item that is now combined with, or accompanied by, the subject.

The objection might be:

A: “How was that cut mark on the door made?”

B: “It was made by the murderer.”

Pedantically, B is inaccurate as murderers tend not to be sharp. It should be

B’: “It was made by the murderer’s knife.

Compare:

(iii) He dug the garden with a spade.

(iv) He dug the garden with a song in his heart.

(v) He dug the garden with his wife.

All are correct and describe what/who was with him whilst he dug. In (iii) the reader assumes the instrumental, (he may have been holding a spade whilst operating a rotivator) but not with (iv) and (v).