You're only meant to be able to swap out redundant proficiencies from your background
The rule in question that allows changing redundant proficiencies to begin with (which is presumably why DDB has implemented it in any form) is under the "Proficiencies" heading of the "Backgrounds" section of the rules. The rule states:
Each background gives a character proficiency in two skills. [...]
In addition, most backgrounds give a character proficiency with one or
more tools. [...]
If a character would gain the same proficiency from two different
sources, he or she can choose a different proficiency of the same kind
(skill or tool) instead.
(The omitted portions simply indicate other sections of the rules, where skills and tools are listed.)
As noted in my answer to a related question about what skills can be chosen for the Knowledge cleric's Blessings of Knowledge feature - as well as in Medix2's answer to a question specifically about whether the rule applies to proficiencies granted by any source at any level - this rule is meant to apply only to proficiencies granted by your background (which only happens at character creation, at 1st level). It's not a general rule that applies whenever a skill or tool proficiency might be redundant; if it were, it would probably appear in a more general rules section, not specifically in the "Backgrounds" section of the rules.
In addition, there are no mechanics for retraining proficiencies (skill or tool) from your background if you gain the same proficiency again from another source (e.g. a class or subclass feature) after 1st level.
...So D&D Beyond's behavior in this regard is a bug
Given the above, this is an error on D&D Beyond's part. It is likely intended to make it easy for players to create characters following the order in "Chapter 1: Step-By-Step Characters"; the character builder is designed in the same order, so players will be prompted to choose their class (and the skill/tool proficiencies from their class) before they choose their background (and gain the corresponding skill/tool proficiencies from that background).
The bug is presumably a result of DDB's system checking whether such a proficiency is granted by the character's class (in any way - rather than only the character's initially chosen class at 1st level), and then making sure that proficiency can't be chosen for the background. As such, I suspect that if any class feature you gain at a later point grants that proficiency (as in your case), it erroneously forces that tool (or skill) proficiency to be deselected for your background.
In any case, it's seemingly a result of the character manager not being designed to account for the relevant rule only applying to a redundant proficiency from your background at 1st level - basically, D&D Beyond's character builder likely wasn't designed to apply the rule so narrowly, for whatever reason. However...
This bug makes it easy to apply a house-rule that says otherwise
The developers of D&D Beyond likely do not see this as an important enough problem to warrant redesigning the system to restrict the ability to do that, especially when many DMs already house-rule to allow retraining redundant proficiencies from any source anyway.
As such, depending on whether your DM house-rules to allow you to reallocate the redundant proficiency or not, you can either leave the background tool proficiency "unselected" in D&D Beyond's character builder (if your DM sticks to the intended limitation of the rule), or reassign your background tool proficiency to something else (if your DM house-rules to let you can do so).