On broad level, Section 38 explains what will be made available as 'information' to recipient of supplies, including 'details of inward supplies in respect of which credit of input tax may be available to the recipient'.
And Section 41 (1) deals with availment of ITC subject to such conditions and restrictions as may be prescribed, as self-assessed. Section 41 (2) deals with a scenario where the tax payable whereon has not been paid by the supplier.
Section 38 (broadly speaking, information made available in Form GSTR-3B) is one of many facets (i.e. conditions / restrictions etc.) before one becomes eligible to avail ITC. And, same cannot be read as sole basis of taking any ITC.
And various provisions (including Section 16 & 17 as well) needs to be read harmoniously with each other (unless & until same is just not possible despite just & reasonable efforts).
Summarizing above, I do not see any apparent contradiction between Section 38 & Section 41.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.