In Text Analytic Tools for Semantic SimilarityText Analytic Tools for Semantic Similarity, they developed a algorithm in order to find the similarity between 2 sentences. But if you read closely, they find the similarity of the word in a matrix and sum together to find out the similarity between sentences. So, it might be a shot to check word similarity.
Also in SimLex-999: Evaluating Semantic Models With (Genuine) Similarity Estimation, they explain the difference between association
and similarity
which is probably the reason for your observation as well. For example, coffee and a cup. They are not similar but they are associative. So just considering similarity would give a different result. The authors suggest various models to estimate them.