It is worth pointing out that native speakers of Latin were well aware of the ambiguity referred to by Joonas in his question (directional/locative prefix IN- vs. negative prefix IN-). For example, consider the ambiguity of invocatus ('called upon' and 'not called upon') that is comically exploited by Plautus in the following text (Pl. Capt. 1, 69ff.):
Iuventus nomen indidit Scorto mihi,
eo quia invocatus soleo esse in convivio.
Scio absurde dictum hoc derisores dicere,
at ego aio recte. Nam scortum in convivio
sibi amator, talos quom iacit, scortum invocat.
Estne invocatum an non est? est planissume;
verum hercle vero nos parasiti planius,
quos numquam quisquam neque vocat neque invocat,
quasi mures semper edimus alienum cibum;
For relevant discussion of the ambiguity of invocatus involved in 'called upon' (directional IN- + vocatus) and 'not called upon' (negative IN- + vocatus), please read the following note 1 contained in this English translation (The Comedies of Plautus. Henry Thomas Riley. London: G. Bell and Sons, 1912).
1 Because invocated: "Invocatus." The following Note is extracted from Thornton's Translation of this Play:--"The reader's indulgence for the coinage of a new term (and perhaps not quite so much out of character from the mouth of a Parasite) is here requested in the use of the word 'invocated' in a sense, which it is owned, there is no authority for, but without it no way occurs to explain the poet's meaning--which, such as it is, and involved in such a pun, is all that can be aimed at. The word 'invocatus' means both 'called upon' and 'not called upon.' Ergasilus here quibbles upon it; for, though at entertainments he attends, as it is the common character of Parasites to do, without invitation, that is 'not called upon;' and as mistresses are 'called upon' that their names so invoked may make their lovers throw the dice with success; still, according to the double sense of the word, they may be compared to each other, as they are both, according to the Latin idiom, 'invocati.'"
NB I: A couple of ambiguous words like the ones commented on by Tom Cotton and cnread are: oratio inscripta est ((I) NEG in-: 'the speech is unwritten' and (II) DIR/LOC in-: 'the speech was inscribed/signed' (e.g., with the author's name)) & inauratus ((I) NEG in-: 'not ornamented with gold' or (II) DIR/LOC in-: perf. pass. participle of inaurare 'to cover with gold').
NB II: I think it is also interesting to point out that in Latin there are very few examples of co-appearance of the negative prefix IN- with the directional/locative IN-. For example, the three ones found in Baldi (1989: 6) are: ininventibilis, ininvestigabilis, and ininvicem. Cf. this link for a more complete list.